Compositions and methods for altering gene expression

ABSTRACT

Provided herein are improved compositions and methods for the directed control of gene expression.

CROSS-REFERENCE TO RELATED APPLICATION(S)

This application claims the benefit of U.S. Provisional Application No. 62/234,770, filed Sep. 30, 2015. The entire teachings of the above application is incorporated herein by reference.

GOVERNMENT SUPPORT

This invention was made with government support under Grant Number HG002668 awarded by the National Institutes of Health. The government has certain rights in the invention.

FIELD OF THE INVENTION

The present invention generally relates to methods of selectively altering gene expression within, for example, insulated neighborhoods formed by the looping of two CTCF interaction sites occupied by cohesion.

REFERENCE TO LENGTHY TABLE

The specification includes lengthy Tables: Table S1E and Table S2A. Lengthy Table S1E has been submitted via EFS-Web in electronic format as follows: File name: S1ETBL.txt, Date created: Sep. 30, 2016; File size: 2,482,827 Bytes and is incorporated herein by reference in its entirety. Lengthy Table S2 has been submitted via EFS-Web in electronic format as follows: File name: S2ATBL.txt, Date created: Sep. 30, 2016; File size: 360,209 Bytes and is incorporated herein by reference in its entirety.

Please refer to the end of the specification for access instructions.

BACKGROUND OF THE INVENTION

Embryonic stem cells depend on active transcription of genes that play prominent roles in pluripotency (ES cell identity genes) and on repression of genes encoding lineage-specifying developmental regulators (Ng and Surani, 2011; Orkin and Hochedlinger, 2011; Young, 2011). The master transcription factors (TFs) OCT4, SOX2, and NANOG (OSN) form super-enhancers at most cell identity genes, including those encoding the master TFs themselves; these super-enhancers contain exceptional levels of transcription apparatus and drive high-level expression of associated genes (Hnisz et al., 2013; Whyte et al., 2013).

Maintenance of the pluripotent ESC state also requires that genes encoding lineage-specifying developmental regulators remain repressed, as expression of these genes can stimulate differentiation and thus loss of ESC identity. These repressed lineage specifying genes are occupied by polycomb group proteins in ESCs (Boyer et al., 2006; Lee et al., 2006; Margueron and Reinberg, 2011; Squazzo et al., 2006). The ability to express or repress these key genes in a precise and sustainable fashion is thus essential to maintaining ESC identity.

Recent pioneering studies of mammalian chromosome structure have suggested that they are organized into a hierarchy of units, which include topologically associating domains (TADs) and gene loops (FIG. 1A) (Dixon et al., 2012; Filippova et al., 2014; Gibcus and Dekker, 2013; Naumova et al., 2013; Nora et al., 2012).

TADs, also known as topological domains, are defined by DNA-DNA interaction frequencies, and their boundaries are regions across which relatively few DNA-DNA interactions occur (Dixon et al., 2012; Nora et al., 2012). TADs average 0.8 Mb, contain approximately seven protein-coding genes, and have boundaries that are shared by the different cell types of an organism (Dixon et al., 2012; Smallwood and Ren, 2013). The expression of genes within a TAD is somewhat correlated, and thus some TADs tend to have active genes and others tend to have repressed genes (Cavalli and Misteli, 2013; Gibcus and Dekker, 2013; Nora et al., 2012).

Gene loops and other structures within TADs are thought to reflect the activities of transcription factors (TFs), cohesin, and CTCF (Baranello et al., 2014; Gorkin et al., 2014; Phillips-Cremins et al., 2013; Seitan et al., 2013; Zuin et al., 2014). The structures within TADs include cohesin-associated enhancer-promoter loops that are produced when enhancer-bound TFs bind cofactors such as Mediator that, in turn, bind RNA polymerase II at promoter sites (Lee and Young, 2013; Lelli et al., 2012; Roeder, 2005; Spitz and Furlong, 2012). The cohesin-loading factor NIPBL binds Mediator and loads cohesin at these enhancer-promoter loops (Kagey et al., 2010). Cohesin also becomes associated with CTCF-bound regions of the genome, and some of these cohesin-associated CTCF sites facilitate gene activation while others may function as insulators (Dixon et al., 2012; Parelho et al., 2008; Phillips-Cremins and Corces, 2013; Seitan et al., 2013; Wendt et al., 2008).

The chromosome structures anchored by Mediator and cohesin are thought to be mostly cell-type-specific, whereas those anchored by CTCF and cohesin tend to be larger and shared by most cell types (Phillips-Cremins et al., 2013; Seitan et al., 2013). Despite this picture of cohesin-associated enhancer-promoter loops and cohesin-associated CTCF loops, we do not yet understand the relationship between the transcriptional control of cell identity and the sub-TAD structures of chromosomes that may contribute to this control. Furthermore, there is limited evidence that the integrity of sub-TAD structures is important for normal expression of genes located in the vicinity of these structures.

To gain insights into the cohesin-associated chromosome structures that may contribute to the control of pluripotency in ESCs, we generated a large cohesin ChIA-PET data set and integrated this with other genome-wide data to identify local structures across the genome.

The results show that super enhancer-driven cell identity genes and repressed genes encoding lineage-specifying developmental regulators occur within insulated neighborhoods formed by the looping of two CTCF interaction sites occupied by cohesin.

Perturbation of these structures demonstrates that their integrity is important for normal expression of genes located in the vicinity of the neighborhoods.

SUMMARY OF THE INVENTION

The present disclosure provides compositions and methods for regulating gene expression in a directed fashion.

In one embodiment is provided a method of altering the expression of a gene in an insulated neighborhood (IN) of the genome of a cell comprising contacting an organism comprising said cell with a gene modulatory molecule. Such molecules include, but are not limited to, small molecules, lipid, proteins, peptides, nucleic acids, such as RNA, DNA or any modified version thereof, and combinations thereof.

In one embodiment, expression of the gene is increased.

In one embodiment, the cell is selected from the group consisting of stem cells, bone marrow cells, testis cells, olfactory cells, lung cells, thymus cells, cells of the central nervous system, cells of the brain, spleen cells, MEF cells, MEL cells, heart cells, somatic cells of the limbs, liver cells, and kidney cells.

In one embodiment, the cells are stem cells and said stem cells are embryonic stem cells.

In one embodiment, the insulated neighborhood comprises a topologically active domain (TAD).

In one embodiment, the topologically active domain is a super-enhancer domain (SD) and such SDs may be selected from any known SD or any disclosed herein such as those in Table S4A and S4B.

In one embodiment, the gene is selected from the group consisting of those in Table S4C.

In one embodiment is provided a method of altering the expression of a gene located in an insulated neighborhood (IN) of the genome of a cell comprising altering the sequence of one or more of the CTCF boundaries of said insulated neighborhood.

In one embodiment, the CTCF boundary is altered via CRISPR technology.

Such alteration may involve either or both of the boundaries of the insulated neighborhood.

Additional embodiments of the present compositions and methods, and the like, will be apparent from the following description, drawings, examples, and claims. As can be appreciated from the foregoing and following description, each and every feature described herein, and each and every combination of two or more of such features, is included within the scope of the present disclosure provided that the features included in such a combination are not mutually inconsistent. In addition, any feature or combination of features may be specifically excluded from any embodiment of the present invention. Additional aspects and advantages of the present invention are set forth in the following description and claims, particularly when considered in conjunction with the accompanying examples and drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

FIG. 1 DNA Interactions Involving Cohesin (A) Units of chromosome organization. Chromosomes consist of multiple topologically associating domains (TADs). TADs (image adapted from Dixon et al., 2012) contain multiple genes with DNA loops involving interactions between enhancers, promoters, and other regulatory elements, which are mediated by cohesin (blue ring) and CTCF (purple balls). Nucleosomes represent the smallest unit of chromosome organization. (B) Heatmap representation of ESC ChIP-seq data for SMC1, a merged data set for the transcription factors OCT4, SOX2, and NANOG (OSN), MED12, RNA polymerase II (Pol2), H3K27me3, and CTCF at SMC1-occupied regions. Read density is displayed within a 10 kb window, and color scale intensities are shown in rpm/bp. Cohesin occupies three classes of sites: enhancer-promoter sites, polycomb-occupied sites, and CTCF-occupied sites. (C) ESC cohesin (SMC1) ChIA-PET data analysis at the Mycn locus. The algorithm used to identify paired-end tags (PETS) is described in detail in the Extended Experimental Procedures. PETs and interactions involving enhancers and promoters within the window are displayed at each step in the analysis pipeline: unique PETs, PET peaks, interactions between PET peaks, and high-confidence interactions supported by at least three independent PETs and with a false positive likelihood of <1% (see Extended Experimental Procedures). (D) Summary of the major classes of interactions and high-confidence interactions identified in the cohesin ChIA-PET data. Enhancers, promoters, and CTCF sites where interactions occur are displayed as blue circles, and the size of the circle is proportional to the number of regions. The interactions between two sites are displayed as gray lines, and the thickness of the gray line is proportional to the number of interactions. The diagram on the left was generated using the interactions, and the diagram on the right was generated using the high-confidence interactions. See also Figures S1 and S2 and Tables S1 and S2.

FIG. 2 DNA Interactions Frequently Occur within Topologically Associating Domains. (A) An example TAD shown with normalized Hi-C interaction frequencies is displayed as a two-dimensional heat map (Dixon et al., 2012), and the TAD is indicated as a gray bar. High-confidence SMC1 ChIA-PET interactions are depicted as blue lines. (B) Enrichment of CTCF, cohesin (SMC1), and PET peaks at TAD boundary regions. The metagene representation shows the number of regions per 10 kb window centered on the TAD boundary, and ±500 kb is displayed. (C) Pie chart of high-confidence interactions that either fall within TADs (88%) or across TAD boundaries (12%). (D) High-confidence interactions are displayed as a two-dimensional heatmap across a normalized TAD length for the ˜2,200 TADs (Dixon et al., 2012). The display is centered on the normalized TAD and extends beyond each boundary to 10% of the size of the domain. See also Table S3A.

FIG. 3 Super-Enhancer Domain Structure. (A) An example super-enhancer domain (SD) within a TAD. High-confidence SMC1 ChIA-PET interactions are depicted as blue lines. ChIP-seq binding profiles (reads per million per base pair) for CTCF, cohesin (SMC1), and the master transcription factors OCT4, SOX2, and NANOG (OSN) are shown at the Lefty1 locus in ESCs. The super-enhancer is indicated by a red bar. (B) Model of SD structure. The 197 SDs have interactions (blue) between cohesin-occupied CTCF sites that may serve as outer boundaries of the domain structure. SDs also contain interactions between super-enhancers and the promoters of their associated genes. (C) Metagene analysis showing the occupancy of various factors at the key elements of TADs and SDs, including CTCF sites, super-enhancers, and super enhancer-associated genes. ChIP-seq profiles are shown in reads per million per base pair. Boundary site metagenes are centered on the CTCF peak, and ±2 kb is displayed. Super-enhancer metagenes are centered on the 197 super-enhancers in SDs, and ±3 kb is displayed. The data for associated genes are centered on the 219 super-enhancer-associated genes in SDs, and ±3 kb is displayed. (D) Heatmap showing that cohesin ChIA-PET high-confidence interactions occur predominantly within the SDs. The density of high-confidence interactions is shown across a normalized SD length for the 197 SDs. (E) Heatmap showing that transcriptional proteins are contained within boundary sites of SDs. The occupancy of Mediator (MED12), H3K27ac, and RNA polymerase II (Pol2) at super-enhancers and associated genes is shown across a normalized SD length for the 197 SDs. See also Figure S3 and Table S4.

FIG. 4 Super-Enhancer Domains Are Functionally Linked to Gene Expression. CRISPR-mediated genome editing of CTCF sites at five loci. The top of each panel shows high-confidence interactions depicted as blue lines and ChIP-seq binding profiles (reads per million per base pair) for CTCF, cohesin (SMC1), and OCT4, SOX2, and NANOG (OSN) in ESCs at the respective loci. The super enhancer is indicated as a red bar. The bottom of each panel shows gene expression level of the indicated genes in wild-type and CTCF site-deleted cells measured by qRT-PCR. Transcript levels were normalized to GAPDH. Gene expression was assayed in triplicate in at least two biological replicate samples and is displayed as mean+SD. All p values were determined using the Student's t test. (A) CRISPR-mediated genome editing of a CTCF site at the miR-290-295 locus (p<0.001, Pri-miR-290-295, and Nlrp12 in wild-type versus CTCF site-deleted). (B) CRISPR-mediated genome editing of a CTCF site at the Nanog locus (p<0.05, Nanog in wild-type versus CTCF site-deleted). (C) CRISPR-mediated genome editing of a CTCF site at the Tdgf1 locus (p<0.001, Gm590; p<0.01, Lrrc2) in wild-type versus CTCF site-deleted). (D) CRISPR-mediated genome editing of a CTCF site at the Pou5f1 locus (p<0.012, H2Q-10 in wild-type versus CTCF site-deleted). (E) CRISPR-mediated genome editing of CTCF sites at the Prdm14 locus (p<0.001, Slco5a1 in wild-type versus CTCF site-deleted). The CTCF-deletion lines at the Pou5f1 and Prdm14 (C1-2) loci are heterozygous, whereas the CTCF-deletion lines at the Nanog, Tdgf1, and miR-290-295 loci are homozygous for the mutation. See also Figure S4.

FIG. 5 Polycomb Domain Structure. (A) An example polycomb domain (PD) within a TAD. A high-confidence interaction is depicted as the blue line. ChIP-seq binding profiles (reads per million per base pair) for CTCF, cohesin (SMC1), and H3K27me3 at the Gata2 locus in ESCs. (B) Model of PD structure. The 349 PDs have interactions (blue) between CTCF sites that serve as putative boundaries of the domain structure. (C) Metagene analysis reveals the occupancy of various factors at the key elements of TADs and PDs: CTCF sites and target genes. ChIP-seq profiles are shown in reads per million per base pair. Boundary site metagenes are centered on the CTCF peak, and ±2 kb is displayed. The metagenes depicting genes are centered on the 380 polycomb target genes in PDs, and ±3 kb is displayed. (D) Heatmap showing that high-confidence interactions are largely constrained within PDs. The density of high-confidence interactions is shown across a normalized PD length for the 349 PDs. (E) Heatmap showing that polycomb proteins are contained within boundary sites of PDs. The occupancy of CTCF, H3K27me3, SUZ12, and EZH2 is indicated within a 20 kb window centered on the left, and right CTCF-occupied boundary region is shown for the 120 PDs with this transition pattern. (F) CRISPR-mediated genome editing of a CTCF site at the Tcfap2e locus. (Top) A high-confidence interaction is depicted by a blue line, and ChIP-seq binding profiles (reads per million per base pair) for CTCF, cohesin (SMC1), and H3K27me3 are shown in ESCs. (Bottom) Expression level of the indicated genes in wildtype and CTCF site-deleted cells measured by qRT-PCR. Transcript levels were normalized to GAPDH. Gene expression was assayed in triplicate in at least two biological replicate samples and is displayed as mean+SD (p<0.05, Tcfap2e in C1 deletion cells; p<0.001, Tcfap2e in C2 deletion cells in wild-type versus CTCF site-deleted). p values were determined using the Student's t test. See also Figure S5 and Table S5.

FIG. 6 Insulated Neighborhoods Are Preserved in Multiple Cell Types. (A) Model depicting constitutive domain organization, mediated by interaction of two CTCF sites co-occupied by cohesin, in two cell types. (B) An example SD in ESCs and a domain in NPCs. High-confidence interactions from the SMC1 ChIA-PET data set are depicted by blue lines, and 5C interactions from Phillips-Cremins et al. (2013) are depicted by black lines. Super-enhancers are indicated by red bars. ChIP-seq binding profiles (reads per million per base pair) for CTCF, cohesin (SMC1), OCT4, SOX2, NANOG (OSN), SOX2, and BRN2 are shown at the Nanog locus and the Olig1/Olig2 locus in ESCs and NPCs. (C) Occupancy of CTCF peaks across 18 cell types. The CTCF peaks used for the analysis are the CTCF peaks found in ESCs. The percentage of these peaks that are observed in the indicated number of cell types is shown for four groups of CTCF sites: all CTCF peaks identified in ESCs, CTCF peaks at SD boundaries in ESCs, CTCF peaks at PD boundaries in ESCs, and CTCF peaks at PET peaks (identified by SMC1 ChIA-PET in ESCs). See also Figure S6 and Table S3B.

FIG. 7 (Figure S1). PET Quality Assessment and Interactions, Related to FIG. 1. (A) Heatmap representation of ESC ChIP-seq data for the combination of the master transcription factors OCT4, SOX2 and NANOG (OSN), MED12, RNA polymerase II (Pol2), CTCF, and SMC1 at promoters and enhancers in ESCs. Read density is displayed within a 10 kb window and color scale intensities are shown in rpm/bp. (B) Heatmap representation of ESC ChIP-seq data for the combination of the master transcription factors OCT4, SOX2 and NANOG (OSN), MED12, RNA polymerase II (Pol2), CTCF, and SMC1 at CTCF-bound sites in ESCs. Read density is displayed within a 10 kb window and color scale intensities are shown in rpm/bp. (C) Scatter plot showing the number of non self-ligation PETs in 10 kb windows in replicates in reads per million mapped reads per kilobase. (D) Bar graph showing the percentage of high confidence interactions from one replicate of the SMC1 ChIA-PET supported by interactions in the other replicate. (E) Left, scatter plot showing the frequency of non-chimeric PETs with homodimeric linkers against PET genomic span in increments of 100 bp. The curve suggests a distance cut-off at 4 kb, below which the PETs may originate from self-ligation of DNA ends from a single chromatin fragment in the ChIA-PET protocol. Right, scatter plot showing chimeric PET frequencies with heterodimeric linkers against PET genomic span in increments of 100 bp, suggesting chimeric PETs were more uniformly distributed across different genomic spans. (F) Bar graph showing the percentage of interactions called by requiring different numbers of chimeric and non-chimeric PETs. All PET interactions called using chimeric PETs that are supported by at least 3 PETs have a false positive likelihood <1% (see Extended Experimental Procedures). (G) Diagram showing the frequency of intrachromosomal and interchromosomal interactions in the interaction (left) and high confidence interaction data set (right). (H) Saturation analysis of the SMC1 ChIA-PET data set. Subsampling of various fractions of PETs within the merged ChIA-PET data set was performed, and the number of unique genomic positions of intrachromosomal PETs beyond the self-ligation distance cutoff of 4 kb was plotted. The solid line depicting the non-linear least-squares regression fitting of the data to the Michaelis-Menten model suggests that we have sampled approximately 70% of the available intrachromosomal PETs beyond 4 kb in the current library. The dashed line indicates the estimated 100% saturation.

FIG. 8 (Figure S2) High-Confidence SMC1 ChIA-PET Interactions Are Consistent with Previously Identified Interactions, Related to FIG. 1. High-confidence SMC1 ChIA-PET interactions are depicted as blue lines. Interactions from other published data sets are depicted as black lines. ChIP-seq binding profiles (reads per million per base pair) for CTCF, cohesin (SMC1), and OCT4, SOX2, and NANOG (OSN) are shown at the indicated loci in ESCs. (A) A high-confidence SMC1 ChIA-PET interaction is supported by 3C from (Kagey et al., 2010). Genomic coordinates for the Lefty1 TAD are chr1:182,760,000-183,160,000. Genomic coordinates for the Lefty1 ChIP-seq binding profiles are chr1:182,851,700-182,871,500. (B) A high-confidence SMC1 ChIA-PET interaction is supported by a CTCF ChIA-PET PET from (Handoko et al., 2011). Genomic coordinates for the Prdm14 TAD are chr1:13,040,000-13,680,000. Genomic coordinates for the Prdm14 ChIP-seq binding profiles are chr1:13,034,300-13,131,900. (C) A high-confidence SMC1 ChIA-PET interaction is supported by a Pol2 ChIA-PET PET in (Zhang et al., 2013). Genomic coordinates for the Phc1 TAD are chr6:121,160,000-122,600,000. Genomic coordinates for the Phc1 ChIP-seq binding profiles are chr6:122,241,500-122,350,700. (D) A high-confidence SMC1 ChIA-PET interaction is supported by 5C in (Phillips-Cremins et al., 2013). Genomic coordinates for the Sox2 TAD are chr3:33,680,000-35,520,000. Genomic coordinates for the Sox2 ChIP-seq binding profiles are chr3:34,522,100-34,691,600.

FIG. 9 (Figure S3) Super-Enhancer Domains, Related to FIG. 3. Active cell identity genes reside in Super-enhancer Domains (SD). Shown are example SDs within Topologically Associating Domains (TADs) in ESCs. High confidence SMC1 ChIA-PET interactions are depicted as blue lines. ChIP-seq binding profiles (reads per million per base pair) for CTCF, cohesin (SMC1), and the master transcription factors OCT4, SOX2, and NANOG (OSN) are shown at the example SDs in ESCs. Super-enhancer regions are indicated by a red bar. (A) Genomic coordinates for the Sox2 TAD are chr3:35,520,000-33,680,000. Genomic coordinates for the Sox2 binding profiles are chr3:34,724,900-34,502,100. (B) Genomic coordinates for the Prdm14 TAD are chr1:13,040,000-13,680,000. Genomic coordinates for the Prdm14 binding profiles are chr1:13,034,300-13,131,900. (C) Genomic coordinates for the Sall1 TAD are chr8:90,920,000-92,360,000. Genomic coordinates for the Sall1 binding profiles are chr8:91,455,200-91,581,300. (D) Genomic coordinates for the Klf9 TAD are chr19:22,920,000-24,360,000. Genomic coordinates for the Klf9 and binding profiles are chr19:23,068,300-23,273,400. (E) Genomic coordinates for the Id1 TAD are chr2:152,440,000-152,680,000. Genomic coordinates for the Id1 binding profiles are chr2:152,511,000-152,581,000. (F) Genomic coordinates for the Pou5f1 TAD are chr17: 35,600,000-36,080,000. Genomic coordinates for the Pou5f1 binding profiles are chr17:35,617,300-35,649,800. (G) Genomic coordinates for the Trim28 TAD are chr7:13,000,000-13,640,000. Genomic coordinates for the Trim28 binding profiles are chr7:13,590,396-13,620,304. (H) Genomic coordinates for the Elovl6 TAD are chr3:128,920,000-129,480,000. Genomic coordinates for the Elovl6 binding profiles are chr3:129,217,096-129,348,924. (I) Genomic coordinates for the Txnip TAD are chr3:96,320,000-96,520,000. Genomic coordinates for the Txnip binding profiles are chr3:96,347,300-96,391,100. (J) Genomic coordinates for Hs6st1 TAD are chr1:34,520,000-36,360,000. Genomic coordinates for Hs6st1 binding profiles are chr1:35,883,900-36,200,400.

FIG. 10 (Figure S4) Super-Enhancer Domain Functions, Related to FIG. 4. (A) Quantitative 3C analysis at the miR-290-295 locus. The super-enhancer domain is indicated as a black bar. The deleted CTCF site is highlighted with a box. Arrows indicate the chromosomal positions between which the interaction frequency was assayed. Asterisk indicates the 3C anchor site. ChIP-seq binding profiles (reads per million per base pair) for CTCF, cohesin (SMC1), and the master transcription factors OCT4, SOX2, and NANOG (OSN) are also shown. The super-enhancer is indicated as a red bar. The interaction frequencies between the indicated chromosomal positions and the 3C anchor sites are displayed as a bar chart (mean+SD) on the bottom panel. qPCR reactions were run in duplicates, and values are normalized against the mean interaction frequency in wild-type cells. (p<0.05 for all three regions; Student's t test.) (B) Quantitative 3C analysis at the Pou5f1 locus. The super-enhancer domain is indicated as a black bar. The deleted CTCF site is highlighted with a box. Arrow indicates the chromosomal positions between which the interaction frequency was assayed. Asterisk indicates the 3C anchor site. ChIP-seq binding profiles (reads per million per base pair) for CTCF, cohesin (SMC1), and the master transcription factors OCT4, SOX2, and NANOG (OSN) are also shown. The super enhancer is indicated as a red bar. The interaction frequencies between the indicated chromosomal positions and the 3C anchor sites are displayed as a bar chart (mean SD) on the bottom panel. qPCR reactions were run in duplicates, and values are normalized against the mean interaction frequency in wild-type cells. (p<0.05; Student's t test.) (C) Expression level of the indicated germ layer markers in wild-type cells and a cell line where the SD boundary CTCF site was deleted at the miR-290-295 locus. Gene expression was measured by qRT-PCR. Gene expression was assayed in triplicate reactions in at least two biological replicate samples and is displayed as mean+SD (p value <0.003, PAX6, GATA6 and Sox17 in wild-type versus CTCF site-deleted). p value was calculated using the Student's t test.

FIG. 11 (Figure S5) Polycomb Domain Interactions, Related to FIG. 5. Repressed developmental lineage genes reside in chromosome structures termed Polycomb Domains (PD). Example PDs within Topologically Associating Domains (TADs) are shown with high-confidence PET interactions depicted by blue lines. ChIP-seq binding profiles (reads per million per base pair) for CTCF, cohesin (SMC1), and H3K27me3 are shown at the example PDs in ESCs. (A) Genomic coordinates for the Tlx1 TAD are chr19:45,120,000-45,840,000. Genomic coordinates for the Tlx1 binding profiles are chr19:45,178,400-45,246,700. (B) Genomic coordinates for the Lhx4 TAD are chr1:157,400,000-158,640,000. Genomic coordinates for the Lhx4 binding profiles are chr1:157,392,000-157,657,700. (C) Genomic coordinates for the Ihh TAD are chr1:74,240,000-75,600,000. Genomic coordinates for the Ihh binding profiles are chr1:74,978,200-75,060,400. (D) Genomic coordinates for the Onecut3 TAD are chr10:79,200,001-81,040,000. Genomic coordinates for the Onecut3 binding profiles are chr10:79,892,959-79,985,160. (E) Genomic coordinates for the Rax TAD are chr18:66,080,001-66,680,000. Genomic coordinates for the Rax binding profiles are chr18:66,089,130-66,130,404. (F) Genomic coordinates for the Shh TAD are chr5:28,760,001-29,680,000. Genomic coordinates for the Shh binding profiles are chr5:28,766,181-28,808,422. (G) Genomic coordinates for the Dhh TAD are chr15:98,360,001-100,560,000. Genomic coordinates for the Dhh binding profiles are chr15:98,718,426-98,738,916. (H) Genomic coordinates for the Fendrr/Foxf1 TAD are chr8:123,160,001-124,360,000. Genomic coordinates for the Fendrr/Foxf1 binding profiles are chr8:123,482,102-123,627,553. (I) Genomic coordinates for the Bhlhe22 TAD are chr3:17,800,001-19,120,000. Genomic coordinates for the Bhlhe22 binding profiles are chr3:17,927,749-18,082,958. (J) Genomic coordinates for the Adamtsl5 TAD are chr10:79,200,001-81,040,000. Genomic coordinates for the Adamtsl5 binding profiles are chr10:79,797,646-79,818,602.

FIG. 12 (Figure S6) SD and PD Boundary Sites Are Constitutively Occupied by CTCF across Multiple Cell Types, Related to FIG. 6. The proportions of SDs and PDs identified in ESCs for which CTCF ChIP-seq peaks at both boundaries are observed in other mouse cell types. Occupancy of CTCF peaks across the cell types was determined from publicly available CTCF ChIP-seq data (Shen et al., 2012). MEF cells are murine embryonic fibroblasts and MEL cells are murine erythroleukemia cells.

DETAILED DESCRIPTION

Provided herein are compositions and methods for the controlled or selected regulation of gene expression such as those genes found in insulated neighborhoods within the genome.

As used herein, an “insulated neighborhood” is a region of a chromosome bounded by one or more markers.

Modulation of gene expression in an insulated neighborhood can be effected by administration of a gene modulatory compound.

In one embodiment, administration of a gene modulatory compound increases the level of gene expression by 5%, 10%, 15%, 20%, 25%, 30%, 33%, 35%, 40%, 45%, 50%, 52% 55%, 60%, 65%, 67%, 69%, 70%, 74%, 75%, 76%, 77%, 80%, 85%, 90%, 95% or more than 95%.

In one embodiment, gene expression may be increased by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 21, 22, 23, 24, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 1-5, 1-10, 1-20, 1-30, 1-40, 1-50, 2-5, 2-10, 2-20, 2-30, 2-40, 2-50, 3-5, 3-10, 3-20, 3-30, 3-40, 3-50, 4-6, 4-10, 4-20, 4-30, 4-40, 4-50, 5-7, 5-10, 5-20, 5-30, 5-40, 5-50, 6-8, 6-10, 6-20, 6-30, 6-40, 6-50, 7-10, 7-20, 7-30, 7-40, 7-50, 8-10, 8-20, 8-30, 8-40, 8-50, 9-10, 9-20, 9-30, 9-40, 9-50, 10-20, 10-30, 10-40, 10-50, 20-30, 20-40, 20-50, 30-40, 30-50 or 40-50 times the wild type level or such level as is presented by a subject having a disease or disorder associated with the aberrant expression of that gene.

Discussion of Results

Understanding how the ESC pluripotency gene expression program is regulated is of considerable interest because it provides the foundation for understanding gene control in all cells. There is much evidence that cohesin and CTCF have roles in connecting gene regulation and chromosome structure in ESCs (Cavalli and Misteli, 2013; Dixon et al., 2012; Gibcus and Dekker, 2013; Gorkin et al., 2014; Merkenschlager and Odom, 2013; Phillips-Cremins and Corces, 2013; Phillips-Cremins et al., 2013; Sanyal et al., 2012; Sofueva et al., 2013) but limited knowledge of these structures across the genome and scant functional evidence that specific structures actually contribute to the control of important ESC genes.

We describe here organizing principles that explain how a key set of cohesin-associated chromosome structures contributes to the ESC gene expression program. To gain insights into the relationship between transcriptional control of cell identity and control of chromosome structure, we carried out cohesin ChIA-PET and focused the analysis on loci containing super-enhancers, which drive expression of key cell identity genes.

We found that the majority of super enhancers and their associated genes occur within large loops that are connected through interacting CTCF sites co-occupied by cohesin. These super-enhancer domains, or SDs, typically contain one super-enhancer that loops to one gene within the SD. The SDs appear to restrict super-enhancer activity to genes within the SD because the cohesin ChIA-PET interactions occur primarily within the SD and loss of a CTCF boundary tends to cause inappropriate activation of nearby genes located outside that boundary.

The proper association of super-enhancers and their target genes in such “insulated neighborhoods” is of considerable importance, as the mistargeting of a single super enhancer is sufficient to cause leukemia (Groschel et al., 2014). The cohesin ChIA-PET data and perturbation of CTCF sites suggest that genes that encode repressed, lineage-specifying, developmental regulators also occur within insulated neighborhoods in ESCs. Maintenance of the pluripotent ESC state requires that genes encoding lineage-specifying developmental regulators are repressed, and these repressed lineage-specifying genes are occupied by nucleosomal histones that carry the polycomb mark H3K27me3 (Boyer et al., 2006; Bracken et al., 2006; Lee et al., 2006; Ne'gre et al., 2006; Schwartz et al., 2006; Squazzo et al., 2006; Tolhuis et al., 2006).

The majority of these genes were found to be located within a cohesion-associated CTCF-CTCF loop, which we call a polycomb domain (PD). The perturbation of CTCF PD boundary sites caused derepression of the polycomb-bound gene within the PD, suggesting that these boundaries are important for maintenance of gene repression within the PD. CTCF has previously been shown to be associated with boundary formation, insulator activity, and transcriptional regulation (Bell et al., 1999; Denholtz et al., 2013; Felsenfeld et al., 2004; Handoko et al., 2011; Kim et al., 2007; Phillips and Corces, 2009; Schwartz et al., 2012; Sexton et al., 2012; Soshnikova et al., 2010; Valenzuela and Kamakaka, 2006).

Previous report shave also demonstrated that cohesin and CTCF are associated with large loop substructures within TADs, whereas cohesin and Mediator are associated with smaller loop structures that sometimes form within the CTCF-bound loops (de Wit et al., 2013; Phillips-Cremins et al., 2013; Sofueva et al., 2013). CTCF-bound domains have been proposed to confine the activity of enhancers to specific target genes, thus yielding proper tissue-specific expression of genes (DeMare et al., 2013; Handoko et al., 2011; Hawkins et al., 2011).

Our genome-wide study extends these observations by connecting such structures with the transcriptional control of specific super-enhancer-driven and polycomb-repressed cell identity genes and by showing that these structures can contribute to the control of genes both inside and outside of the insulated neighborhoods that contain key pluripotency genes.

The organization of key cell identity genes into insulated neighborhoods may be a property common to all mammalian cell types. Indeed, several recent studies have identified CTCF-bound regions whose function is consistent with ESC SDs (Guo et al., 2011; Wang et al., 2014).

For example, in T cell acute lymphocytic leukemia, Notch1 activation leads to increased expression of a super-enhancer-driven gene found between two CTCF sites that are structurally connected but does not affect genes located outside of the two CTCF sites (Wang et al., 2014).

Future studies addressing the mechanisms that regulate loop formation should provide additional insights into the relationships between transcriptional control of cell identity genes and control of local chromosome structure.

The following examples of the related art and limitations related therewith are intended to be illustrative and not exclusive. Other limitations of the related art will become apparent to those of skill in the art upon a reading of the specification and a study of the drawings.

Compounds useful in the invention include those described herein in any of their pharmaceutically acceptable forms, including isomers such as diastereomers and enantiomers, salts, solvates, and polymorphs, as well as racemic mixtures and pure isomers of the compounds described herein, where applicable.

While a number of exemplary aspects and embodiments have been discussed herein, those of skill in the art will recognize certain modifications, permutations, additions and sub-combinations thereof. It is therefore intended that the following appended claims and claims hereafter introduced are interpreted to include all such modifications, permutations, additions and sub-combinations as are within their true spirit and scope.

All patents, patent applications, patent publications, scientific articles and the like, cited or identified in this application are hereby incorporated by reference in their entirety in order to describe more fully the state of the art to which the present application pertains.

EQUIVALENTS AND SCOPE

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments in accordance with the invention described herein. The scope of the present invention is not intended to be limited to the above Description, but rather is as set forth in the appended claims.

In the claims, articles such as “a,” “an,” and “the” may mean one or more than one unless indicated to the contrary or otherwise evident from the context. Claims or descriptions that include “or” between one or more members of a group are considered satisfied if one, more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process unless indicated to the contrary or otherwise evident from the context. The invention includes embodiments in which exactly one member of the group is present in, employed in, or otherwise relevant to a given product or process. The invention includes embodiments in which more than one, or the entire group members are present in, employed in, or otherwise relevant to a given product or process.

It is also noted that the term “comprising” is intended to be open and permits but does not require the inclusion of additional elements or steps. When the term “comprising” is used herein, the term “consisting of” is thus also encompassed and disclosed.

Where ranges are given, endpoints are included. Furthermore, it is to be understood that unless otherwise indicated or otherwise evident from the context and understanding of one of ordinary skill in the art, values that are expressed as ranges can assume any specific value or subrange within the stated ranges in different embodiments of the invention, to the tenth of the unit of the lower limit of the range, unless the context clearly dictates otherwise.

In addition, it is to be understood that any particular embodiment of the present invention that falls within the prior art may be explicitly excluded from any one or more of the claims. Since such embodiments are deemed to be known to one of ordinary skill in the art, they may be excluded even if the exclusion is not set forth explicitly herein. Any particular embodiment of the compositions of the invention (e.g., any nucleic acid or protein encoded thereby; any method of production; any method of use; etc.) can be excluded from any one or more claims, for any reason, whether or not related to the existence of prior art.

All cited sources, for example, references, publications, databases, database entries, and art cited herein, are incorporated into this application by reference, even if not expressly stated in the citation. In case of conflicting statements of a cited source and the instant application, the statement in the instant application shall control.

Section and table headings are not intended to be limiting.

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EXAMPLES

The following examples are illustrative in nature and are in no way intended to be limiting.

Example 1. Experimental Procedures A. Experimental Procedures Cell Culture

V6.5 murine ESCs were grown on irradiated murine embryonic fibroblasts (MEFs) under standard ESC conditions, as described previously (Whyte et al., 2012). V6.5 murine ESCs were grown on irradiated murine embryonic fibroblasts (MEFs). Cells were grown under standard ESC conditions as described previously (Whyte et al., 2012). Cells were grown on 0.2% gelatinized (Sigma, G1890) tissue culture plates in ESC media; DMEM-KO (Invitrogen, 10829-018) supplemented with 15% fetal bovine serum (Hyclone, characterized SH3007103), 1,000 U/ml LIF (ESGRO, ESG1106), 100 μM nonessential amino acids (Invitrogen, 11140-050), 2 mM L-glutamine (Invitrogen, 25030-081), 100 U/ml penicillin, 100 μg/ml streptomycin (Invitrogen, 15140-122), and 8 nl/ml of 2-mercaptoethanol (Sigma, M7522).

Genome Editing

The CRISPR/Cas9 system was used to create ESC lines with CTCF site deletions. Target-specific oligonucleotides were cloned into a plasmid carrying a codon-optimized version of Cas9 (pX330, Addgene: 42230). The genomic sequences complementary to guide RNAs in the genome editing experiments were:

Name Sequence SEQ ID NO PRDM14_C1_up ATGACATAATGAGATTCACG PRDM14_C1_down ACTGAAGTGGAAGGTGAGTG PRDM14_C2_down CGACCCACCTCCTAACCTTA MIR290_C1_up CATTGGCTGTCAACTATACC MIR290_C1_down CCCGTCCTAAATTATCTGCG POU5F1_C1_up CAGAAGCTGACAACACCAAG POU5F1_C1_down ACACTCAAACTCGAGGACTC NANOG_C1_up TTAAACACATCATAAGATGA NANOG_C1_down TGAACTACGTAGCAAGTTCC TDGF1_C1_up CAGTCTGAACTGCACATAGC TDGF1_C1_down AAAGCTAAACTCTCCCAAGT TCFAP2E_C1_up CCACGTGGGAAATCTAACTC TCFAP2E_C1_down GAAGTGAAGCCTTCTCGTTA TCFAP2E_C2_up GAAGAGTGTGACTGAAAAGA TCFAP2E_C2_down TCTCACGGAGCCTCAGGAGA

Cells were transfected with two plasmids expressing Cas9 and sgRNA targeting regions around 200 base pairs up- and downstream of the CTCF binding site, respectively. A plasmid expressing PGK-puroR was also cotransfected, using X-fect reagent (Clontech) according to the manufacturer's instructions. One day after transfection, cells were replated on DR4 MEF feeder layers. One day after replating, puromycin (2 ug/ml) was added for 3 days. Subsequently, puromycin was withdrawn for 3-4 days. Individual colonies were picked and genotyped by PCR.

For the Prdm14 (C1-2), mir-290-295, Pou5f1 and Nanog SDs and Tcfap2e (C1) PD boundary CTCF site deletions, at least two independent clones were expanded and analyzed. Data on FIGS. 4, 5 and S4 were obtained from the analysis of a single representative clone for each genotype. The sequences of the deletion alleles in the used cell lines are listed below.

PRDM14 Locus Reference Sequence:

CCGTTTCCCTAGCACAGAGCCACCCAGGACCAGAAATAACAGCTTCACAA AAGAGCTCGCTCTGTACACATGGGTCCCAAGGAAGAAGTGAGATTCTTTC CCCCTCACTGAGGAAAGGGGGCCGTCTTTCCTGCTAAAGAGAAAGAAAGT GAAGTTTCCTGGAATCTTCTTTTTCTCCTCGTGAATCTCATTATGTCATC GAAATTCTAGGCTTAATCGATGCTTCTGCCCCAGCTTCTCAATTATCTGA GATTTCAGATGCCCACCGCGTCCAGCTCAGAAAATCAAATTGTGGTTACT ATTCTAGACATTTCCAGCAGAGGGCGCTTCGGTGCAGGTAGCCAGAACAC CGAAGTCATCCAGTTTCTGGCCGCAAACTCAGATTACTAGATTGCCAACA GGGTTTCCAGAACGTGGGTAAAAGAGACTGAAGTGGCAATCCCCACGAAA ACAAAAAAAACAAAACAAAACGGTCAAGGGTGCTTCGTACTGAAGTGGAA GGTGAGTGAGGCTGTGTGGGCAGATCGCAACCGTCATTTAGAACAAACCT GAAGCAGAGCGGTGTAAATGACTGTATTCCCAGCACTCAAGAGAATAGCT GGAGCTTTGGCCAGCCTACAGAGGAGACCCTGTGCTGTTCTCAGTATTCA GTTATGCTACCCTCTAATGAAGTACATTGTACTTCCTGGTAATTTCATTT TTATGAAAGGCAATACTGGATTCCTGCCTTTCTTCCTTTCTGCCTGTAGT CCGTTTTTAGGTTGATCAACAGGTTGACATTACACTTGTGACAATTCTCT TGCCTCACGGAACGATAACGTTTCAAAGGGGAAGACTAATTAGGATTGGT ACCGTTAGTTTTTTGTCAACACAGCCAGAGTCATCTGGGAAGAGGGAACC TGAGCTGGGGGTTTACCTCCATCAGATCGTTTGTGAGTATGTCTGTAGGA AATGTTCTTAATCATTAATATCGGAGAGCCAGACCATCCCCGGTGGTGCC ACTGCTGGGCCGGTAGTCCTGGGTGATACAAGGAGGCAGGTTTACTGGCT AGTAAGCAGCACTCCTTTGCAGGCTCTGCTCCACTCTCTCCTTCCTCCCT TCTGCCTTGAGTTCCTGTCTTGACTTCCCTCGGTGATGAGCTGTACCCTG AAAACCAGATAACTTGTCCTTAATTTACTTTTGGTCATGGTAGACTTTTT ATTATTGTTGTTTTGTTGTTGTTGTTGTTGTTGTTGTTTTTATGTGTATG GGTGTTTTGCTTACAAGTATGTCTGGGCACCATATTCATGCACAGTGATG CCCAATGATTCCAGAAAAGGGCCGAGGATTCCCTGGGACTGGAGTTACAG AAAGTTAGGAGCTGCCATGTGTGTGCAGCGAATCAAACTCTGGCCTTCTG GAAGAGCAGCCAGTGCTCTTAACTGCTGATCCATCTTTCTAGCCCACTTC GTCACGTTGTTTATCACAGCAGTCGAAAGCAGACTAGGACATGATGGAAA GGAGTCAAAAGCTTGGTCAAGGGATCTTTAGAGATGGGAAGGGGAACTTT TTAAACGTTGGTCCTGCCATGCTCTCCCAGAGGCATGGTGCCTTCTCTGT CTTTCCTAGTGCTTTCCTTTGCAAAGCAAGCAAATATCATCTACTTTGGT GTTTTAAGAAATAGTACGGGGGGGCTGGTGAGATGGCTCAGTGGGTTAGA GCACCCGACTGCTCTTCCGAAGGTCCAGAGTTCAAATCCCAGCAACCACA TGGTGGCTCACAACCATCCGTAACGAGATCTGACTCCCTCTTCTGGTGTG TCTGAAGACAGCTACAATGTACTTACATATAATAAATAAATAAATCTTTA AAAAAAAAAAAAAAAAAAAAAAAAGAAATAGTACGGGGCTGGTGAGATGG CTTAGTGGGTAAAAGCACCCGACTGCTCTTCCGAAGGTTCAAAGTTCAAA TCCCAGCAACCACATGGTGGCTCACAATCACCCGTAATGAGATCTGACTC CCTCTTCTGAAGTGTCTAAAGACAGCTACAGTGTACATTATATGTAATAA ATAAATGTTTTTTTMAAAAAGAAAGAAATAGTACATTTCTCAATGGCCTC GAGAATTAACCTGCAGGAAAAGGAAAATGCTGTGTTTCTTCTCCAAAAAT CCTATAGGTGGCGCACAGACACCGGTTTCAAGTGATGGGTCCCAGCTTTG ACCTTTCTGCCCAAGTCCGGTTTGTCGGGAACTCTTCTTCCTTCTGCCTC TACCCCCTGCCAGAATTACAGGGCTGCTCTTGGCTCTGAGTTGTTCGGTG TAAGTGAGAAAGCAAGCAGCACCTGCAGTCCTGAGGTGTCACCTAGCAGC TCCCTTCTAACAAGGCTGCGCTCCTCTTGGGAGGACATAGCCAAGAGTCA CTGAAGGGCAAGCTCCCTCAAAGCTCCTCTCTAAGGTTAAATAGCAGCAT GACCTCGACCCACCTCCTAACCTTAAGGTTCATATTCTCTCTGCAAAACA TCAAGGGGGTCTGGAGGAACACTGAAGTCCCTCCTGCCGCATG

PRDM14 C1-2 Deletion Allele Sequence:

TCTCCTGCTAAAGAGAAAGAAAGTGAAGTTTCCTGGAATCTTCTTTTTCT CCTCCACCTCCTAACCTTAAGGTTCATATTCTCTCTGCAAAACATCAAGG GGGTCTGGAGGAACACTG

MIR290 Locus Reference Sequence:

CCAGGCCTCACTAGTGTCAGGTCGTGAGTCATGCACAGCCATGATTTCTG CATCCTTGGCCACCTTGCTCAGTTTTCTGGAGTGTTGAGATTCAATGCGA ACACCACCACAGCTGGGCAAAATCTAATAACCCAGGATAGGATGGGAGCA TTGGCTGTCAACTATACCAGGTGTGCAAATCTTGGGTTTTGAGGCCTCAT TTGTAAGGTGCCTTATACCTTTAGCCCCAGCCCACTTTTTTTTCCCCCTG CTGTATAAAATTCAGGTGTGAGTACAATTTTTCTTTTTAAAGATTTATAA GTGTTCTGTAGCTATCTTCAGATTCACCCAAAGAAGGCATTGGATCCCAT TACAGATGATTGCAAGCCACCATGTAGTTGCTGGGAATTGAACTCAGGAC CTCTGACTTAACCACTCCAGCCCTTGAGTACAATTTTTGAAAAATTACCT TGTGGGTCTTTATGCTGTGACTTGGCCAGTAGATGGCAGTCTTGGTCCAT GGAAATGTCTAGGACTCTGGATATTTTTCCTTTTCTGTGGTCTTTACTGA TCTTCAAACCTGCTAACCAGCCAATCCCCGTCCTAAATTATCTGCGTGGA ATCTACATCAAACCCAGTGAGCTCCATCAAAGGTTGAGTGTTTAGGTCTC AAGCAGAACAATTTTGTCAACCTGCACTTACTGGGCCTCCTGACCTAAGA CGGTCCCATGTAACAGGATGACCTTGAGTGATCTTGTCTCCACCTCACCA TATACCAGAGGCTGGCCTTTAAAAGTTCCACCTCAAGTGCTTCAAAGCA

MIR290 C1 Deletion Allele Sequence:

AAATCTAATAACCCAGGATAGGATGGGAGCATTGGCTGTCAATCTATATC AAACCCAGTGAGCTCCATCAAAGGTTGAGTGTTTAGGTCTCAAGTAGAAC AATTTTGTCAACCTGCACTTACTGGGCCTCCTGACCTAAGACGGTCCCAT GTAACAGGAT

POU5F1 Locus Reference Sequence:

CTCAGCCATCTCCCTGTTGAGCTGTCAAGCAGAGAGGCCCCAACAACAAC ACAGGAAATTGCCAGTGTTCTTGATTGCCCAAAAGAACCAGATGACCAGA AGCTGACAACACCAAGAGGCTAGGGGTCTTCCAGTTGGCCTTGTACTGTT GCAACTGTCAGGGAAAGGATGTAACCAGAGGGCCTCTGGGACTCCTCTCA CCCTTGATAGTTTGAGGGATATGAGCAAATTACACGGTTATCAGAAGGTG GCCATAGTGACACTGAAAATTGGCCCATTGGCTTCAAAGATTTACCAAAG TACCGTCCGTATTTTCTACCTACGGTGTGCTGGAGCCTAGAGGACACTAG GGGGCGCGCTGAGCTCGCGGAAGCCACCCAGAGTCCTTCCAGGAGACTCC CTTAAAGGTTGATCAAATTGTTCTTTGCCAAACTGAATTTATCATAAAAA TTATACTTTATTTTGTATTACTTTGTGTACATGGGTGTTTTGCCTTCACA GATGCGTCTGGTGCACCTGAGAAGCCAGAAAAGAGAACAGGAGTGAACAG GTTTGTGGGGGCTGACACTCAAACTCGAGGACTCTGGGAAAGCATCGAGT GCTCTTAACCATTGAGCCATCTCTCCAGCCCATCTGTTTTCTTTTGCCGG AGGAAGGGGCTCTGAGAAAGGATCTTACCTGTAGCCCAGGCTGGCCCAGT TCACCATGTGATGAAGGCTCCTTTCAAATCCAAGCTA

POU5F1 C1 Deletion Allele Sequence:

AATTGCCAGTGTTCTTGATTGCCCAAAAGAACCAGATGACCAGAAGCTGA CAACAAATTATACTTTATTTTGTATTACTTTGTGTACATGGGTGTTTTGC CTTCACAGATGCGTCTGGTGCACCTGAGAAGCCAGAAAAGAGAACAGGAG TGAACAGGTTTGT

NANOG Locus Reference Sequence:

TCAGTTGTGTGTGGGGTAGGCCATGTGTGCCTTGGTGCACATGTGCAGGT CAGAACAACTTGGGTGAGAGTCTGCTTCCTTTTTCTGCTCTGTATGGGTT GTAGGGATAGAATTCAAGTTTCGCATTTGAATTCTATGGTTTAGCACTTA AACATCAAAACCTTTCCCAGAACGTCACACTTCAATGCCATTGAGGAAGG TGTCTGTAACGCTGTGTGTGTGTTGTTAGTTAAACACATCATAAGATGAA GGAAAGCTGGGAGTGTCCTTAACACAGCAGCGAGCAGCAAAAGCTACTTT CTCCTCAAGCCTGGAGGAGTCTGGTCCGACAGTCCACCAACAGGGGGCGT TATTTCCCAGCCCTCGTGAAGCGTTGAACTGTCCTGGTGAGAAGGGTGAT GTGCAGTTCCTTGTCTCAGCAGCAGATGGAGCCATAGGGACGAGAACAAG TTCCTAGGTGAAGGAAGGAGTGGGGGGAGACGAAGCGGAAGAAGCTGAAG TGCATCTTGGTCGGTCAAATTTTTCTTATTGATGAAAAAGATGATTAAAG GACACTGTGAATTTGAGACTATTCTGAACTACGTAGCAAGTTCCAGGACA GCCAGTGTTACAAATCAAGACCCGATTTTGGAAGAAGATGGGGGCTGGGG AAGGCGCCATGTTCCCCCCCCCACCCCCCACCCCCAGCTCCCATCTCATC TGTTGCTACATTTACTAGACTGCCAAGAATTTTCTCTCTCAGAAATTAAA AAAATAGTAAAGAAATAAAGAAAAAAGCCAGGCATGATGGTTCACTCTCA TAATCCCATAATTCCATTACGTAAGAGAATCTCTCTACC

NANOG C1 Deletion Allele Sequence:

GTCTGTAACGCTGTGTGTGTGTTGTTAGTTAAACACATCATAAGATCCAG GACAGCCAGTGTTACAAATCAAGACCCGATTTTGGAAGAAGATGGGGGCT G

TDGF1 Locus Reference Sequence:

TGAGCAACAAGATGTCTGCACCATCTTTTCATCCCTCGGATTTTTCTTTA TAGTCGTGGCTTGTACTGAGTAGACAGGTTCCTGTCTCTGACAAAAACGG AGGACAGAAACCCCACTCTTCTCCAAAGAAGCATGCTGATAAAAAGTGGA CACAAACCATGAACTGCCGTGTGACAGTCTGAACTGCACATAGCCGGATG AGGCTTTCGGGTAAAGACTAGAATTGCAAGATTACTAACACTGTTAAACT CTTTGTTTTCTGCAGTCCTTGGTTTAGACTCAAGACTCTGAAACCTAGAA ACTGAGCTCAAGGCTTCCGAGGCTTTGACATCGAAACACCTGATCTCCAG TAGGGGGCGCTGCAGCCTAGCAGGGCGGAGCTGACTCTTCTGGCCAGTTT TTTCTCCTGATGGTCCCAGTAAAACTCATGTCAGGCTCAGATTTTAGACT AAGGGACTGGAAAGGGGGAATTCTGAGAATTAGAGCTAAAGAATTAGAGG GGTTAAAGAGTGAAGCCCAGGAAAATATATTTGAACAAATAAAAGCTAAA CTCTCCCAAGTTGGACAAACAAAAACAAAACAAAAACCCTCCATAAATCC TCAATCTTTAGCTTCAAGAAATTGAATCCAAAGGAACCCATATCCAGACC CGGTGCTCAGCGTGGAAAAGGCCAGAGTGCTGAAAGCAGCTGACTCTTCA GTACACATGGACAAACCCTGGCAGAGCTGGGCAAGAAAACAGACACACCT GGGTGTGATAATGACTT

TDGF1 C1 Deletion Allele Sequence:

AGACAGGTTCCTGTCTCTGACAAAAACGGAGGACAGAAACCCCACTCTTC TCCAAAGAAGCATGCTGATAAAAAGTGGACACAAACCATGAACTGCCGTG TGACAGTCTGAACTGGACAAACAAAAACAAAACAAAAACCCTCCATAAAT CCTCAATCTTTAGCTTCAAGAAATTGAATCCAAAGGAACCCATATCCAGA CCCGGTGCTCAGCGTGGAAAAGG

TCFAP2E Locus Reference Sequence (C1):

GCTATCTTGCATCTAGAAGTGGAAAGACAGTTCTTTAAATGCCTAGGCAG TGTACATTAACCTATGACAAGCAAACACTCCCCTGTGGATTTTGCTCTTC AGTTTGCCTGTATGTATGTGTGCTTGTATTTGCACTGCATGTGTTTCTGG TGCCCTTGAAGATCAGAAGAAACATCAAACCCCCTAGGACTAGAGTTACA GATGGCTGTGAATCACCACGTGGGAAATCTAACTCTGGACTTGGGGGGGT GTGTATTGAGAGAGTAATTTTTAGAAGAAAGAAGACAAGCAGGGTAGGAC AGAAAATTTTTAAAAAGCTGGAAAGAATGTAATCTCATATGATTTTATAG GATAAAATTTTAAGGTACAAATGGGACCACAGAATTAGTTCCCCACATGA GCAAGATGGTCTTCTGTATTATTATTTTTTTTCCTTTTATGGTGTTTTGT CTGCATGTGTGTCTGTGCACCATGTGCATGAAGTGCCTGAGAAGGCCAGC AGAGGGCATCAGATCCCTTGAGATGAGTTACAGGTGGTTGAGAGACACCT TATGAGTCCTGGAAATTATACCTGGGTACTCTGGAAGAGCAGCCAGGATT CTTAACCTCTGAGCCATCTCCCTGGCCCCAATCTTTTGCATTCTTCTGTC CGTCAGCTATTCAATCCATTTCAAAGTGGAAGTGAAGCCTTCTCGTTAAG GATGACAGTTATCCGGAAGGGAGCATGAAAATGTTCCAGGGCCTTTTCTT GCTTTATGCACACTCAAAGCTGAAAATCTTTCCCATGTCAATGGATGAGA CCATCACTCAATACCTAAACAGAAAACTATGAAGCCTAATTGCTTGTGTG CTTGCTTAAGTATATACTGGTTGGTGACAGCTTCCACCAAGAAAGGCATA CCACTGATTGATAACATTGGTAACAACATGAACTTCAGGTATTGATAGGT T

TCFAP2E C1 Deletion Allele Sequence:

TGCACTGCATGTGTTTCTGGTGCCCTTGAAGATCAGAAGAAACATCAAAC CCCCTAGGACTAGAGTTACAGATGGCTGTGAATCACCACGTGGGATGACA GTTATCCGGAAGGGAGCATGAAAATGTTCCAGGGCCTTTTCTTGCTTTAT GCACACTCAAAGCTGAAAATCTTTCCCATGTCAATGGATGAGACCATCAC TCAATACCTAAACAGAAAACTAT

TCFAP2E Locus Reference Sequence (C2):

TGATCCACTTCCAGCTCCTTGGTTCATTCAGCATCTTTCACCTGGCCCAT GCCCCTCCCCTTATGCAAAATGCCTCCGGGATCATGGCCTTGGCCCACTC CAGGAATGAAGCTGACTAGCACTCCAGGACTCCTGGTTACTTTTCCTTTC TTGCTCTGTGAGTCGCTTCACCAGAAGTCTAAAGTTGGGGGGGAGGGGGG GGGGGAAGAGTGTGACTGAAAAGATGGCTCAGAGGCTACGAGAACCGGCT GCTCTTTCAAAGGAGTCAGGTTTCATCCCCAGTACCCACATGGCAGGAAT GGCTATCTGTAATTCCAGTTCTGATGGATCTGGTGAGTCTGACGCCCTCT TCTGGCCCCCACAGGCATTGCGCTGCACAGACAGGCTGGCAGAACACCCC ACACATAAAACAATAAAGGAATCTTTAAAAAAAAAAAAAAGTCTAAAGAA GTCACAAGTCGGGCTGGTGAGATGGCTCAGTGGGTAAGAGCACCCGACTG CTCTTCCAAAGGTCCGGAGTTCAAATCCCAGCAACCACATGGTGGCTCAC AACCATCCATAATGAGATCTGACGCCCTCTTAAGTGTCTGAAGACAGCTA CAGTGTACTTACATATAATAAATAAATAAATCTAAAAAAAAAAAAGTCAA AAGTCTATTTAGTACTTTGCTTGGAGTGGGTCAAGCAGCCAACAAATAGC TACTAAATAAATAAGTAACCAAAAAGATAATTACAGTTTTCCAAATCTGT TAGGGGACTCTTTGGAAGGGCTCTTATGTGACCTTGACCTAGCATAGCTA CACATAAGGCCCAGTTATAAGTGAGCACAAACGAGCAACTGTGCTTATTT CTTCTAGGAGGGACATGTGCTTCATGAGCTACTTCTCTGGAGACCAGCAG AGCTGTGGAATACCAGGGTTTCAGACTGGGCCCTTCTGTTTCAGGGGCAA GGGTTCTTCACATTGTAAGCATGCAGGTGATGATTTCTTATGGTTTTATT TTATTTTTTTTTTTTAGATACAGACACCTGGATGAAGGCATGAGGAAGGC AGAGAGATACCCCTGGGAAAACGGAGACCACAACAGGCACAGATACACTG ATAAGACATATATACACATCGGTATGCATGCTCAAATACACATGGACTCT CAGTTGACATTCTTGGCTTATTCTCTTCCAAGGCTCACGTTTTCTCCTCT TTAAAACAAAACAAAACGAAACGAAACGAAACAAAACAAACAAACAAACC CCAAACTTTTTTGTCCTCCTTTGTTGACAGAGCCGGATTCCTCTTCCTAA CAGGTCTGTCTGCAAATGTTTGAGATGAAATCTCGCAAAAGATACTGACG CCCCATCTAGTGGCCGGAGCTTACCACTGCAGCTCAACACTCCCCTGCCT GTCTCAGTGGAGGCACCCAGACAGAGCCAGCCCTGCCTTGCAAGCTTCCG CTTAGCCCCTTGCTCACTCTGGAGTCTGGAACCCTCTCACGGAGCCTCAG GAGAAGGCAGGTTTCAGTCTGCCTTCTGTTCTCAAGCTTCGCTGGCCTTG GCATGCAGGAGAGCAACTCAACCGCAAGGACCGTGGACAGTAATCATTTG CTTTGTGGCCTTTCCCTCACTTCCCCAGACTACCCGTTACTCCCATGATT CCAAAGAACACTTGACAGCTCCCAAATCTGCCTC

TCFAP2E C2 Deletion Allele Sequence:

GGGGGGGAAGAGTGTGACTGCCTTCTGTTCTCAAGCTTCGCTGGCCTTGG CATGCAGGAGAGCAACTCAACCGCAAGGACCGTGGACAGTAATCATT

The CTCF-deletion lines at the Pou5f1 and Prdm14 (C1-2) loci are heterozygous, while the CTCF-deletion lines at the Nanog, Tdgf1, Prdm14 (C1) and miR-290-295 loci are homozygous for the mutation. Gene Expression Analysis ESC lines were split off MEFs for two passages. RNA was isolated using Trizol reagent (Invitrogen) or RNeasy purification kit (Promega), and reverse transcribed using oligo-dT primers and SuperScript III reverse transcriptase (Invitrogen) according to the manufacturers' instructions. Quantitative real-time PCR was performed on a 7000 AB Detection System using the following Taqman probes, according to the manufacturer's instructions (Applied Biosystems).

Gapdh: Mm99999915_g1 Prdm14: Mm01237814_m1 Slco5a1: Mm00556042_m1 Pou5f1: Mm00658129_gH H2-Q10: Mm01275264_g1 Tcf19: Mm00508531_m1 Mmu-mir-292b: Mm03307733_pri Nlrp12: Mm01329688_m1 Myadm: Mm01329822_m1 AU018091: Mm01329669_m1 Nanog: Mm02019550_s1 Dppa3: Mm01184198_g1 Tdgf1: Mm03024051_g1 Gm590: Mm01250263_m1 Lrrc2: Mm01250173_m1 Rtp3: Mm00462169_m1 Tcfap2e: Mm01179789_m1 Psmb2: Mm00449477_m1 Ncdn: Mm00449525_m1 Sox2: Mm03053810_s1 Pax6: Mm00443081_m1 Gata6: Mm00802636_m1 Sox17: Mm00488363_m1

Based on RNA-seq data (Shen et al., 2012), the genes are expressed at the following levels prior to deletion of the CTCF site:

Pou5f1: 79.4 RPKM (rank among 24,827 Refseq transcripts: 232, top 1%)

Prdm14: 2.21 RPKM (rank: 9,745, 39th %)

Slco5a1: 0.93 RPKM (rank: 12,277, 50th %)

miR-295: 18.9 RPKM (rank: 1,902, 8th %)

H2-Q10: 0.48 RPKM (rank: 13,782, 56th %)

Tcf19: 1.03 RPKM (rank: 12,011, 49th %)

Nlrp12: 0.06 RPKM (17,108, 69th %)

AU018091: 17.1 RPKM (rank: 2,150, 9th %)

Myadm: 14.6 RPKM (mean of multiple splice isoforms) (rank: 2610, 11th %)

Dppa3: 25 RPKM (rank: 1,320, 5th %)

Tdgf1: 92 RPKM (rank: 167, top 1%)

Lrrc2: 1.2 RPKM (rank: 10,292, 42nd %)

Rtp3: 0.01 RPKM (rank: 14,587 59th)

Sox2: 122 RPKM (rank: 100, top 1%)

Nanog: 122 RPKM (rank: 99, top 1%)

Pax6: 0.07 RPKM (rank: 16,941, 68th %)

Gata6: 0.25 RPKM (rank: 14,981, 60th %)

Sox17: 0.15 RPKM (rank: 15,754, 64th %)

Psmb2: 85 RPKM (rank: 203, top 1%)

Tcfap2e: 0.19 RPKM (rank: 15,402, 62nd %)

Ncdn: 3.19 RPKM (rank: 8,388, 24th %)

ChIP-Seq Illumina Sequencing and Library Generation

Purified DNA from a H3K27me3 ChIP was used to prepare a library for Illumina sequencing. The library was prepared following the Illumina TruSeq DNA Sample Preparation v2 kit protocol as previously described (Whyte et al., 2012).

Bioinformatics Analysis—ChIP-seq Data Analysis

All ChIP-Seq data sets were aligned using Bowtie (version 0.12.2) (Langmead et al., 2009) to build version MM9 of the mouse genome with parameter -k 1 -m 1 -n 2. Data sets used in this manuscript can be found in Table S6. We used the MACS version 1.4.2 (model-based analysis of ChIP-seq) (Zhang et al., 2008) peak finding algorithm to identify regions of ChIP-seq enrichment over input DNA control. A p value threshold of enrichment of 1e-09 was used for all data sets. For the histone modification H3K27me3 whose signal tends to be broad across large genomic regions, we used MACS (Zhang et al., 2008) with the parameter “-p 1e-09 -no-lambda -no-model”. UCSC Genome Browser (Kent et al., 2002) tracks were generated using MACS wiggle outputs with parameters “-w -S -space=50”.

SMC1 ChIP-Seq

Enrichment Heatmap FIG. 1B, S1A, and S1B shows the average ChIP-seq read density (r.p.m./bp) of different factors at the indicated sets of regions. The average ChIP-seq reads in 50 bp bin were calculated and drawn using bamToGFF (https://github.com/BradnerLab/pipeline). In FIG. 1B, +/−5 kb from the center of the SMC1-enriched region was interrogated. In Figure S1A, the enriched regions of OSN, MED1, and MED12 were merged together if overlapping by at least 1 bp. For each of the merged regions, +/−5 kb from the center of the merged region was interrogated. On Figure S1B, +/−5 kb from the center of the CTCF enriched region was interrogated.

Gene Sets and Classification of Gene Transcriptional State in ESCs

All gene-centric analyses in ESCs were performed using mouse (mm9/NCBI37) RefSeq annotations downloaded from the UCSC genome browser (genome.ucsc.edu). For counting purposes and for assignment of enhancers to target genes (Table S2A-C), we collapsed multiple identical TSS into one gene level TSS. Genes were separated into classes of activity as follows: A gene was defined as active if an enriched region for either H3K4me3 or RNA Pol II was located within +/−2.5 kb of the TSS and lacked an enriched region for H3K27me3 therein. H3K4me3 is a histone modification associated with transcription initiation (Guenther et al., 2007). A gene was defined as Polycomb-occupied if an enriched region for H3K27me3 (representing Polycomb complexes) but not RNA Pol II was located within +/−2.5 kb of the TSS. H3K27me3 is a histone modification associated with Polycomb complexes (Boyer et al., 2006; Lee et al., 2006). A gene was defined as silent if H3K4me3, H3K27me3, or RNA Pol II enriched regions was absent from +/−2.5 kb of the TSS. Remaining genes to which we were unable to assign a state were left as unclassified. Overall, there were 15,312 unique active TSSs, 1,091 unique Polycomb-occupied TSSs, 8,477 unique silent TSSs, and 616 unclassified TSSs in mouse ES cells.

Defining Active Enhancers in ESCs

Co-occupancy of ESC genomic sites by the OCT4, SOX2, and NANOG transcription factors is highly predictive of enhancer activity (Chen et al., 2008) and Mediator is typically associated with these sites (Kagey et al., 2010). We first pooled the reads of ChIP-seq profiles of transcription factors OCT4, SOX2, and NANOG, which were performed in parallel, to create a merged “OSN” ChIP-seq experiment (Whyte et al., 2013). These reads were processed by MACS to create an OSN binding profile for visualization. To define active enhancers, we first identified enriched regions for the merged “OSN” ChIP-seq read pool, and for both Mediator complex components MED1 and MED12 using MACS. Then we used the union of these five sets of enriched ChIP-Seq regions that fell outside of promoters (e.g., a region not overlapping with ±2.5 kb region flanking the RefSeq transcriptional start sites) as putative enhancers.

SMC1 ChIA-PET Processing

All ChIA-PET datasets were processed with a method adapted from a previous computational pipeline (Li et al., 2010). The raw sequences were analyzed for linker barcode composition and separated into non-chimeric PETs with homodimeric linkers (AA or BB linkers) derived from specific ligation products, or chimeric PETs (AB linkers) with heterodimeric linker derived from nonspecific ligation products. We trimmed the PETs immediately before a perfect match of the first 10 nt of the linker sequences (Linker A with CTGCTGTCCG; Linker B with CTGCTGTCAT). After removing the linkers, only the 5′ ends of the trimmed PETs of at least 27 bp were retained, because the restriction enzyme EcoP151 cuts 27 bp away from its recognition sequence.

The sequences of the two ends of PETs were separately mapped to the mm9 mouse genome using the bowtie algorithm with the option “-k 1 -m 1 -v 1” (Langmead et al., 2009). These criteria retained only the uniquely mapped reads, with at most a single mismatch for further analysis. Aligned reads were paired with mates using read identifiers and, to remove PCR bias artifacts, were filtered for redundancy. PETs with identical genomic coordinates and strand information at both ends were collapsed into a single PET. The PETs were further categorized into intrachromosomal PETs, where the two ends of a PET were on the same chromosome, and interchromosomal PETs, where the two ends were on different chromosomes. The two ends of all non-chimeric PETs were used to call PET peaks that represent local enrichment of the PET sequence coverage by using MACS 1.4.2 (Zhang et al., 2008) with the parameters “-p 1e-09 -no-lambda -no-model -keepdup=2”.

Chimeric Versus Non-Chimeric PET Quality Assessment

Chimeric PETs with heterodimeric linkers can be used to estimate the degree of noise in the ChIA-PET dataset. 7% of paired-end ligations involved heterodimeric linkers (AB linkers Table S1A). Since the frequency of ligations involved heterodimeric linkers (AB linkers) gave an estimate of non-specific homodimeric ligations (AA or BB linkers), we estimated that less than 14% of total homodimeric ligations (AA and BB linkers) were nonspecific. We also counted the chimeric PETs that overlapped with PET peaks at both ends by at least 1 bp. These chimeric PETs represented “non-specific” chromatin interactions. We found that more than 99.8% “non-specific” chromatin interactions derived from chimeric PETs overlapping with PET peaks had only 1 chimeric PET; 0.1% “nonspecific” interactions had 2 chimeric PETs. We thus used a 3 PET cut-off for our high-confidence interactions (Figure S1F). Since contact frequency is expected to inversely scale with genomic distance, we examined the relationship between PET frequencies over genomic distance between the two ends of intrachromosomal PETs. The frequency of non-chimeric PETs with homodimeric linkers was plotted over genomic span in increments of 100 bp (Figure S1E). The scatter plot suggested two populations within intra-chromosomal PETs and showed that the vast majority of these PETs were within 4 kb (Figure S1E). We thus used a 4 kb cutoff to remove those PETs that may originate from self ligation of DNA ends from a single chromatin fragment in the ChIA-PET procedure. In contrast, chimeric PETs with heterodimeric linkers did not show an inverse relationship with genomic distance (Figure S1E, Table S1A).

Creation of High-Confidence ChIA-PET Interactions

To identify long-range chromatin interactions, we first removed intrachromosomal PETs of length <4 kb because these PETs may originate from self-ligation of DNA ends from a single chromatin fragment in the ChIA-PET procedure (Figure S1E). We next identified PETs where each end overlapped with a different PET peak (overlap of at least 1 bp).

Operationally, these PETs were defined as putative interactions. Applying a statistical model based upon the hypergeometric distribution identified high-confidence interactions, representing high-confidence physical linking between the PET peaks. Specifically, we first counted the number of PETs originating from each PET peak. We then asked, given the numbers of PETs originating from any two PET peaks, what was the likelihood of seeing the observed number of PETs linking the two PET peaks, using a hypergeometric distribution to generate a p value for each potential interaction. To correct for multiple hypothesis testing, we derived a background distribution for p-values of interactions through random shuffling of the links between PET ends. Using this background distribution, we controlled the number of false positives in our interaction set by setting a p-value cutoff threshold such that only the top 1% of simulated interactions from the background dataset would be called significant. This threshold, which we term the false positive likelihood in figure legends, was then applied to the actual data. This method did not make any assumption of the distribution of p-values as the Benjamini-Hochberg procedure (Benjamini, 1995); both methods for multiple hypothesis testing yielded similar number of interactions (Noble, 2009). For each of the two SMC1 ChIA-PET replicates, two independent PETs were required to call high-confidence interactions between pairs of interacting sites (Table S1C, S1D (not shown); merged data in Table S1E). For the merged SMC1 ChIA-PET dataset, non-chimeric PETs from two replicates were pooled together and three independent PETs were required to call high-confidence interactions (Table S1E).

Saturation Analysis of ChIA-PET Library

To determine the degree of saturation within our ChIA-PET library (Figure S1H), we modeled the number of sampled genomic positions as a function of sequencing depth by the Michaelis-Menten model. Intrachromosomal PETs with a distance span above our self-ligation cutoff of 4 kb were subsampled at varying depths, and the number of unique genomic positions (defined as the start and end coordinates of the paired PETs) that they occupy were counted. Model fitting using non-linear least-squares regression suggested that we have sampled approximately 70% of the available intrachromosomal PET space, encompassing 2.22/3.17 million positions (Figure S1H).

We considered whether ChIA-PET data limitations might limit detection of longer range interactions. If sparseness of data were a significant problem, resulting in under-calling of long-range interactions, we would likely miss previously detected long-range interactions. Instead, we detect previously known long-range interactions, e.g. the interaction between Sonic Hedgehog (Shh) and its enhancer in the intron of the nearby Lmbr1 gene (1 Mb away), interactions between the HoxD gene cluster and its distal regulatory sequences (>300 kb away), and interactions between the HoxA gene cluster and its distal regulatory sequences (>500 kb away) (Lehoczky et al., 2004; Lettice et al., 2003; Spitz et al., 2003).

Reproducibility Analysis of SMC1 ChIA-PET Replicates

Saturation analysis suggested that each of the two SMC1 ChIA-PET replicates sampled only ˜50% of the available intrachromosomal PET space (data not shown). We thus investigated the reproducibility of SMC1 ChIA-PET replicates by examining how often high-confidence interactions from one of the two SMC1 ChIA-PET replicates were supported by PET interactions from the other replicate. Operationally, we counted the percentage of high-confidence interactions from one replicate whose individual end reads overlapped with those from high-confidence interactions identified in the other replicate by at least 1 bp (Figure S1D).

To compare the replicates' genome-wide interaction frequency (Figure S1C), inter-chromosomal PETs and intra-chromosomal PETs below the self-ligation cutoff (4 kb) were filtered. Each chromosome was partitioned into 10 kb bins and 21 symmetric two-dimensional matrices (all bins×all bins) were constructed for each replicate. These matrices were populated such that bin ai,j represented the number of PETs in that replicate with one end in bin i and the other in bin j. PET counts were separately normalized by the number of mapped reads in each replicate as well as the bin size*1000.

This resulted in an RPKM-like metric for all bins in both matrices. Figure S1C represents the relationships between each replicate where the X axis represents bin ai.j in replicate 1 and the Y axis represents bin ai,j in replicate 2. This relationship was also analyzed using the Pearson r.

Assignment of Interactions to Regulatory Elements

To identify the association of long-range chromatin interactions to different regulatory elements, we assigned the PET peaks of interactions to different regulatory elements, including active enhancers, promoters (+/−2.5 kb of the Refseq TSS), and CTCF ChIP-seq binding sites. Operationally, an interaction was defined as associated with the regulatory element if one of the two PET peaks of the interaction overlapped with the regulatory element by at least 1 base-pair.

Assignment of Enhancers to Genes

Our analysis identified 2,921 high-confidence interactions involving an enhancer (contains an OCT4/SOX2/NANOG or MED1 or MED12 enriched region and is not located within +/−2.5 kb of an annotated TSS) and a promoter (+/−2.5 kb of an annotated TSS) (FIG. 1D, Table S1E). Each high-confidence interaction, as defined above, is required to be connected by three PET peaks. A large majority (81%) of these enhancer-promoter interactions (2071/2921 interactions) involved an active gene (H3K4me3 or RNA Pol II but not H3K27me3 enriched regions), while 302 interactions involved a Polycomb-occupied gene (H3K27me3) and 229 interactions involved a silent gene (absence of H3K4me3, RNA Pol II and H3K27me3 enriched regions).

We identified 216 enhancer-promoter interactions that involved super-enhancers (Table S2B), as defined in (Whyte et al., 2013). The high-confidence enhancer-promoter interactions were used to assign super enhancers and typical enhancers to their target genes (Table S2B, S2C). Multiple enhancer constituents that are in close proximity can be computationally stitched together into enhancer regions (true for typical and super-enhancers) as described previously (Hnisz et al., 2013; Whyte et al., 2013).

We identified high confidence interactions overlapping with a super-enhancer or typical enhancer region at one end and a promoter (+/−2.5 kb of a TSS) at the other end (Table S2B, S2C). For 151 super-enhancers with sufficient interaction data, we found that 83% of enhancer assignments to the nearest active gene (including Polycomb-occupied genes) were confirmed/supported by high-confidence interactions.

For typical enhancers with 1477 sufficient interaction data, we found that 87% of enhancer assignments to the nearest active gene (including Polycomb-occupied genes) were confirmed/supported by high-confidence interaction data.

Heatmap Representation of High-Confidence ChIA-PET Interactions at Topologically Associating Domains (TADS)

Genome-wide average representations of ChIA-PET interactions at TADs were created by mapping high-confidence ChIA-PET interactions across TADs (Dixon et al., 2012) (FIG. 2D). All 2,200 TADs plus their upstream and downstream flanking regions (10% of the size of the domain) were aligned and each split into 60 equally-sized bins. To calculate interaction density in each TAD, we first filtered high-confidence interactions by requiring they were completely contained within the genomic region of the TAD and its flanking regions defined above.

We next counted the interaction frequency between any two bins in each TAD to produce a 60 by 60 interaction matrix using a method as previously described in Dixon et al., 2012 The numbers in the interaction matrices represent interaction frequencies at the diagonals originating from two bins on the x- and y-axis. Average interaction frequencies across 2,200 TAD interaction matrices were calculated. The upper triangular matrix of the average interaction frequencies was displayed in the units of interactions per bin in FIG. 2D.

Definition of Super-Enhancer Domains and Polycomb Domains

Typical enhancer and super-enhancer regions in murine embryonic stem cells were described previously (Hnisz et al., 2013; Whyte et al., 2013), and their genomic coordinates were downloaded (Table S2B, S2C). The 231 super enhancers were assigned to genes with a combination of ChIA-PET interactions and proximity to their nearest active transcriptional start sites (TSSs). We first used high-confidence SMC1 PET interactions (FDR 0.01, 3 PETs) between super-enhancers and TSS regions (+/−2.5 kb of a TSS) to identify their target genes.

When super-enhancers did not have PET interactions to any TSS regions, they were assigned the nearest active TSSs (including Polycomb occupied genes) by proximity. Super-enhancers and the TSS regions (+/−2.5 kb of a TSS) of their target genes are considered as SE-gene units. All 231 super enhancers were assigned to target genes with this method. This approach resulted in a total of 302 SE-gene units because a SE occasionally interacted with multiple genes.

We next identified SMC1 PET interactions between two CTCF-enriched regions (regardless of whether these CTCF regions were at promoters or enhancers) that encompass these SE-gene units, which we called super-enhancer domains—we call these regions “CTCF-CTCF PET interactions.” The CTCF-CTCF PET interactions defining super-enhancer domains were required to encompass the TSS regions (+/−2.5 kb of a TSS) and the super enhancer for each SE-gene unit. When multiple nested CTCF-CTCF PET interactions encompassed a SE-gene unit, we used the smallest CTCF-CTCF PET interactions for simplicity.

We identified 193 Super-enhancer Domains (SDs) containing a total of 191 super-enhancers. We noted that the boundaries of super-enhancer are sensitive to the algorithm that computationally defines super enhancers. For 4 super-enhancers, one super-enhancer constituent out of multiple constituent enhancers that define the super enhancers fall outside of the CTCF-CTCF PET interactions. These 4 CTCF-CTCF PET interactions encompass the target gene TSS regions (+/−2.5 kb of a TSS) and more than 50% of the genomic space covered by the super-enhancer. Therefore, we qualified these 4 CTCF-CTCF PET interactions as Super-enhancer Domains.

Thus, we identified a total of 197 Super-enhancer Domains (SDs) containing a total of 197 boundary CTCF-CTCF PET interactions and 195 super-enhancers (Table S4A, S4B). For the ˜15% super-enhancers that did not qualify for occurrence within a SD by using the high confidence ChIA-PET data, the interaction dataset (not the high confidence data) shows that all but one of these super-enhancers are located within CTCF-CTCF loops co-bound by cohesin.

We also performed the same computational analyses for the 8,563 typical enhancers. We found that only 48% (4128/8563) typical-enhancers are contained in CTCF-CTCF topological structures similar to SDs. Developmental regulators in embryonic stem cells frequently exhibit extended binding of Polycomb complex at their promoters spanning 2-35 kb from their promoters (Boyer et al., 2006; Lee et al., 2006). We thus focused on those Polycomb-occupied TSSs that showed enrichment of H3K27me3 spanning greater than 2 kb in size. This distance cutoff was based on analyses performed in (Lee et al., 2006). We noted that ˜60% H3K27me3 regions called by MACS had neighboring H3K27me3 regions within 2 kb. In order to accurately capture the large genomic regions that show enrichment of H3K27me3 signal, we first merged the H3K27me3 regions that were within 2 kb of each other. 546 genes, including 203 encoding transcription factors, showed enrichment of H3K27me3 spanning greater than 2 kb at their promoters.

We next identified high confidence CTCF-CTCF PET interactions that encompassed the H3K27me3 regions of these 546 genes at promoters. When multiple nested CTCF-CTCF PET interactions encompassed the H3K27me3 regions, we took the smallest CTCFCTCF PET interactions for simplicity. We identified 349 Polycomb Domains (PDs) containing a total of 349 boundary CTCF-CTCF PET interactions and 380 Polycomb-associated genes (Table S5A, S5B).

Support for SD and PD Structures from Published Datasets

The existence of Super-enhancer Domains and Polycomb Domains was supported by evidence from published CTCF ChIA-PET datasets (GSE28247) (Handoko et al., 2011). We applied our ChIA-PET processing method to the published CTCF ChIA-PET dataset to identify unique PETs. We then counted the instances where a high-confidence CTCF-CTCF boundary interaction from our ChIA-PET dataset showed a minimum 80% reciprocal overlap with the span of a unique PET from the CTCF ChIA-PET dataset, i.e. 80% of a high-confidence SD boundary interaction region is in common with a CTCF ChIA-PET unique PET and vice versa. To accomplish this, we used BEDtools (https://github.com/arq5x/bedtools2) intersect with parameters -f 0.8 -r -u.

We found that 34% (6770/20080) of our CTCF-CTCF interactions were confirmed by a unique PET within the CTCF ChIA-PET dataset, 33% (65/197) of our SD boundary interactions were confirmed by a unique PET within the CTCF ChIAPET dataset, and 33% (115/349) of our PD boundary interactions were confirmed by a unique PET within the CTCF ChIA-PET dataset (Table S3A). Most Super-enhancer Domains and Polycomb Domains are distinct from the previously described Topologically Associating Domains (TADS).

We compared Super-enhancer Domains and Polycomb Domains to TADs by counting the instances where a Super-enhancer Domain or a Polycomb Domain showed a minimum 80% reciprocal overlap with a TAD. 3% (5/197) of our SDs and 4% (13/349) of our PD have an 80% reciprocal overlap with a TAD (Dixon et al., 2012). 8% (16/197) of our SDs and 9% (30/349) of our PD have an 80% reciprocal overlap with a TAD (Filippova et al., 2014) (Table S3A).

The existence of enhancer-promoter and enhancer-enhancer interactions was supported by evidence from published RNA Pall ChIA-PET datasets (Kieffer-Kwon et al., 2013). We applied our ChIA-PET processing method to the published Pol2 ChIA-PET dataset to identify unique PETs. We then counted the instances where a high-confidence enhancer-promoter or enhancer-enhancer interaction from our Smc1 ChIA-PET dataset showed a minimum 80% reciprocal overlap with a unique PET from the Pol2 ChIA-PET dataset, e.g. 80% of an enhancer-promoter interaction region is in common with a Pol2 ChIA-PET unique PET and vice versa. We found that 82% (2,402/2,921) of our enhancer-promoter interactions were confirmed by a unique PET within the Pol2 ChIA-PET dataset, and 73% (1,969/2,700) of our enhancer-enhancer interactions were confirmed by a unique PET within the Pol2 ChIA-PET dataset (Table S3A).

Several types of structural domains have been previously described, and we expect our interactions to occur largely within their boundaries. Thus, we determined how many of our interactions spanned a boundary. Topologically Associating Domains (TADs) (Dixon et al., 2012) were determined using Hi-C in mouse ESCs; 6% (1,354/23,739) of high-confidence intrachromosomal cohesion-mediated interactions cross a TAD boundary. LOCK (large organized chromatin K9 modification) domains were determined using ChIP data (Wen et al., 2009); 4% (1,053/23,739) of high-confidence, intrachromosomal cohesin-mediated interactions cross a LOCK boundary. Lamin-associated domains (LADS) were determined using DamID (Meuleman et al., 2013); 5% (1,180/23,739) of high confidence intrachromosomal cohesin-mediated interactions cross a LAD boundary (Table S3A).

Meta Representations of ChIP-Seq Occupancy at Super-Enhancer Domains and Polycomb Domains

Genome-wide average “meta” representations of ChIP-seq occupancy of different factors were created by mapping ChIP-seq read density to different sets of regions (FIG. 3C, FIG. 5C). All regions within each set were aligned and the average ChIP-Seq factor density in each bin was calculated to create a meta genome-wide average in units of rpm/bp. For super-enhancers, each super enhancer or their corresponding flanking region (+/−3 kb) was split into 100 equally-sized bins. This split all super-enhancer regions, regardless of their size, into 300 bins. For the target genes within SDs or PDs, we created three regions: upstream, gene body and downstream. 80 equally-sized bins divided the 2000 to 0 promoter region, 200 equally-sized bins divided the length of the gene body, and 80 equally-sized bins divided the 0 to +2 kb downstream region. For SMC1 and CTCF ChIP-Seq binding sites at the SD, PD, and TAD borders, flanking regions (+/−2 kb) around the center of CTCF ChIP-Seq binding sites were aligned and split into 40 equally-sized bins.

Heatmap representations of ChIP-seq read density of different factors were created by mapping the reads within super-enhancers and/or their target genes across super-enhancer domains (FIG. 3E). We first filtered reads for those contacting (>=1 bp) super-enhancers and/or their target genes. Then we created three types of regions: SD and their corresponding flanking regions (+/−10 kb). We divided the upstream and downstream flanking regions into 10 equally-sized bins each. We divided the SD into 50 equally-sized bins. The average filtered ChIP-seq read density (r.p.m./bp) of different factors in each bin was calculated and drawn.

Heatmap Representation of High-Confidence ChIA-PET Interactions Superenhancer Domains and Polycomb Domains

Heatmap representations of ChIA-PET interactions were created by mapping high-confidence ChIA-PET interactions across Super-enhancer Domains (SD) and Polycomb Domains (PD), which are defined above. We created three types of regions: upstream, SD or PD, and downstream. Upstream and downstream regions are 20% of the SD's or PD's length each. We divided the upstream and downstream regions into 10 equally-sized bins each. We divided the SD or PD into 50 equally-sized bins. To calculate interactions in each bin, we filtered high-confidence interactions in two ways. 1) We required high-confidence interactions to have at least one end in the interrogated region. This removed interactions that are anchored outside of our region of interest. 2) We removed interactions that are not related to the internal structure of the domain. This removed interactions that have one end at an SD or PD border PET peak and the other end outside of the SD or PD.

We considered the whole span of each filtered high-confidence ChIA-PET interaction. The density of such spans in each bin was calculated, where all bins contacting an interaction were incremented by 1. Per row counts were normalized by dividing each bin count by the row maximum and displayed in Heatmaps in FIGS. 3D and 5D.

Definition of Putative Chromatin Insulator Elements at the Boundaries of Polycomb Domains

An entropy-based measure of Jensen-Shannon Divergence (JSD) was adopted to identify putative SMC1- and CTCF-bound chromatin insulator elements at PD domain boundaries (FIG. 5E). We divided 20 kb regions centered on CTCF enriched regions within SDs or PDs into 100 equally-sized bins. We used H3K27me3 and SUZ12 ChIP-seq profiles to identify putative insulator elements at PD boundaries. For each 20 kb region, the average ChIP-seq read density within each bin was calculated and the density in each bin was divided by the sum of the row so the new normalized vector sums to 1. Since we expect high ChIP-seq signal at one side of insulator elements and low ChIP-seq signal at other side of insulator elements, we defined two vectors to represent the chromatin patterns at insulator elements at the left or right borders of PDs: one vector has 50 0s followed by 50 1s, and the other has 50 1s followed by 50 0s. These vectors were normalized so their sum was 1.

We next used JSD as described in (Fuglede and Topsoe, 2004) to quantify the similarity between normalized ChIP-seq patterns and the two pre-defined patterns, which results in a similarity score between each normalized ChIP-seq vector and the ideal vectors described above. We took the top 15 percent of our 20 kb regions ranked by their similarity score and extracted those that were at the boundaries of Polycomb Domains (PD). For robustness, only PD border regions whose average ChIP-seq signal (H3K27me3) within the 20 kb window was above the 60 percentile of all CTCF enriched regions at the side within the domain and below 50 percentile of all CTCF enriched regions at the side outside of the domain were considered as putative chromatin insulator elements.

FIG. 5E show normalized ChIP-seq density at these putative chromatin insulator elements by standard Z-transform across all CTCF enriched regions.

Conservation of CTCF Binding Across Cell Types

CTCF peaks in 18 tissues/cell types from ENCODE were downloaded from the UCSC table browser (http://genome.ucsc.edu/cgibin/hgFileUi?db=mm9&g=wgEncodeLicrTfbs).

We restricted our analysis to autosomal CTCF sites, because these 18 cell types could be derived from mice of different sex or strains. We first took the intersection of our autosomal CTCF peaks in murine V6.5 ESC 129-057Bl/6 line and autosomal CTCF peaks in the murine ESC Bruce4 line from ENCODE to account for differences in cells and experimental technique. We next quantified how frequently these autosomal CTCF peaks from ESCs were occupied by CTCF ChIP-Seq peaks in 18 tissues/cell types (including ESC Bruce4 cells) from ENCODE. The histogram of CTCF occupancy across 18 tissues/cell types were plotted in FIG. 6C.

Super-Enhancers in NPCs

Super-enhancers were identified in mouse neural progenitor cells (NPCs) using ROSE (https://bitbucket.org/young_computation/rose). This code is an implementation of the method used in (Hnisz et al., 2013; Loven et al., 2013).

Briefly, regions enriched in H3K27ac signal were identified using MACS with background control, -keep-dup=auto, and -p 1e-9. These regions were stitched together if they were within 12.5 kb of each other and enriched regions entirely contained within +/−2 kb from a TSS were excluded from stitching. Stitched regions were ranked by H3K27ac signal therein.

ROSE identified a point at which the two classes of enhancers were separable. Those stitched enhancers falling above this threshold were considered super-enhancers.

5C CTCF-CTCF Interactions in NPCs

Phillips-Cremins et al. performed 5C at 7 genomic loci (Phillips-Cremins et al., 2013). We filtered for statistically significant 5C interactions in mouse NPC by requiring a p value for both replicates <0.05, resulting in 674 interactions. We filtered for CTCF-CTCF interactions by requiring an overlap with a CTCF ChIPSeq enriched region in NPC on both ends resulting in 32 CTCF-positive 5C interactions. 34% (11/32)

CTCF 5C interactions in NPCs have an 80% reciprocal overlap with a SMC1 ChIA-PET interactions in mouse ESCs (Table S3B).

3C Assays

For each sample, 2×107 ESCs cells were crosslinked with 1% formaldehyde for 20 min at RT. The reaction was quenched by the addition of 125 mM glycine for 5 min at RT. Crosslinked ESCs were washed with PBS and resuspended in 10 ml lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP40 and proteinase inhibitors) and lysed with a Dounce homogenizer. Following BglII digestion overnight, 3C-ligated DNA was prepared as previously described (Lieberman-Aiden et al., 2009).

The 3C interactions at the miR-290-295 and Pou5f1 loci (Figure S4A, S4B) were analyzed by quantitative real-time PCR using custom Taqman probes as previously described (Xu et al., 2011). The amount of DNA in the qPCR reactions was normalized across 3C libraries using a custom Taqman probe directed against the Actb locus. Primer sequences are listed below.

Target Region Primer Name Sequence (5′-3′)

Target, SEQ Region, ID primer name Sequence (5′-3′) NO N1rp12,   CACATCTTCAAAGCAAACACTATTGTT promoter, N1rp12 R N1rp12, Taqman   TCTCCTACCCATTGCTTCTCTGCTACCTGC probe, N1rp12 Probe SE, region 1,  TTCCTGGAACCTGGGCAA N1rp12 eF1 SE, region 2,  TGATACAGCACAGCTTTCCTTCA N1rp12 eF2 SE, region 3,  CAGATTTTTTATTTCCTTCAGTTCTGTG N1rp12 eF3 H2-Q10,   AGGATGGCTCAGCGGTTAAG promoter, H2Q10 F SE region,  AGGGCTCACCTTCAGTCAAGTT H2Q10 R H2-Q10, Taqman   CGGCCTGTCTACTTTAGCCTCAGACTCCA probe, H2Q10 probe Actin, Actin-F GGGAGTGACTCTCTGTCCATTCA Actin, Actin-R ATTTGTGTGGCCTCTTGTTTG A Actin, Taqman   TCCAGGCCCCGCGTGTCC probe, Actin  probe

F, and R denote forward and reverse primers, respectively.

ChIA-PET

In brief, murine ESCs (up to 13×10⁸ cells) were treated with 1% formaldehyde at room temperature for 10 min and then neutralized using 0.2 M glycine. The crosslinked chromatin was fragmented by sonication to size lengths of 300-700 bp. The anti-SMC1 antibody (Bethyl, A300-055A) was used to enrich SMC1-bound chromatin fragments. A portion of ChIP DNA was eluted from antibody-coated beads for concentration quantification and for enrichment analysis using quantitative PCR. For ChIA-PET library construction, ChIP DNA fragments were end repaired using T4 DNA polymerase (NEB) and ligated to either linker A or linker B. After linker ligation, the two samples were combined for proximity ligation in diluted conditions. Following proximity ligation, the paired-end tag (PET) constructs were extracted from the ligation products and the PET templates were subjected to 50 3 50 paired-end sequencing using Illumina HiSeq 2000.

ChIA-PET Library Construction

ChIA-PET was performed as previously described (Chepelev et al., 2012; Fullwood et al., 2009; Goh et al., 2012; Li et al., 2012). Briefly, ES cells (up to 1×10⁸ cells) were treated with 1% formaldehyde at room temperature for 20 min and then neutralized using 0.2M glycine. The crosslinked chromatin was fragmented by sonication to size lengths of 300-700 bp. The anti-SMC1 antibody (Bethyl, A300-055A) was used to enrich SMC1-bound chromatin fragments. A portion of ChIP DNA was eluted from antibody-coated beads for concentration quantification and for enrichment analysis using quantitative PCR.

For ChIA-PET library construction ChIP DNA fragments were end-repaired using T4 DNA polymerase (NEB). ChIP DNA fragments were divided into two aliquots and either linker A or linker B was ligated to the fragment ends. The two linkers differ by two nucleotides which are used as a nucleotide barcode (Linker A with CG; Linker B with AT) (Table S1A). After linker ligation, the two samples were combined and prepared for proximity ligation by diluting in a 20 ml volume to minimize ligations between different DNA-protein complexes. The proximity ligation reaction was performed with T4 DNA ligase (Fermentas) and incubated without rocking at 22 degrees Celsius for 20 hours.

During the proximity ligation DNA fragments with the same linker sequence were ligated within the same chromatin complex, which generated the ligation products with homodimeric linker composition. However, chimeric ligations between DNA fragments from different chromatin complexes could also occur, thus producing ligation products with heterodimeric linker composition. These heterodimeric linker products were used to assess the frequency of nonspecific ligations and were then removed bioinformatically.

As shown in Figure S1E, all heterodimeric linker ligations, giving rise to chimeric PETs, are by definition nonspecific. Because random intermolecular associations in the test tube are expected to be comparable for linkers A and B, the frequency of random homo and heterodimeric linker ligations should also be equivalent. In our SMC1 ChIA-PET library, only 7% of pair-end ligations involved heterodimeric linkers (Table S1A). Thus, we estimate that less than 14% of total homodimeric ligations are nonspecific.

Following proximity ligation, samples were treated with Proteinase K and DNA was purified. An EcoP15I (NEB) digestion was performed at 37 degrees Celsius for 17 hours to linearize the ligated chromatin fragments. The chromatin fragments were then immobilized on Dynabeads M280 Streptavidin beads. An End-Repair reaction was performed (Epicentre #ER81050), then As were added to the ends with Klenow treatment by rotating at 37 degrees Celsius for 35 minutes. Next, Illumina paired-end sequencing adapters were ligated on the ends and 18 cycles of PCR was performed. The Paired-End-Tag (PET) constructs were extracted from the ligation products and the PET templates were subjected to 50×50 paired-end sequencing using Illumina HiSeq 2000. SMC1 ChIA-PET was performed as previously described (Chepelev et al., 2012; Fullwood et al., 2009; Goh et al., 2012; Li et al., 2012).

Data Analysis

ChIA-PET data analysis was performed as previously described (Li et al., 2010), with modifications described in the Extended Experimental Procedures. The high-confidence interactions for the two biological replicate SMC1 ChIAPET experiments and for the merged data set are listed in Tables S1C, S1D (not shown) but merged into Table S1E, respectively. All data sets used in this study are listed in Table S6.

Example 2: Accession Numbers

Raw and processed sequencing data were deposited in GEO under accession number GSE57913 (http://www.ncbi.nlm.nih.gov/geo/).

The GEO accession ID for aligned and raw data is GSE57913 (www.ncbi.nlm.nih.gov/geo/).

Results of Experimentals Cohesin ChIA-PET in ESCs

The organization of mammalian chromosomes involves structural units with various sizes and properties, and cohesin, a structural maintenance of chromosomes (SMC) complex, participates in DNA interactions that include enhancer-promoter loops and larger loop structures that occur within topologically associating domains (TADs) (FIG. 1A). ESC ChIP-seq data indicate that ˜40% of cohesin-occupied sites involve active enhancers and promoters, ˜3% involve genes with polycomb modifications, and ˜50% involve CTCF sites that are not associated with enhancers, promoters, or polycomb-occupied sites (FIG. 1B and Figures S1A and S1B available online). We employed cohesin ChIA-PET to further investigate the relationship between control of the ESC pluripotency program and control of local chromosome structure. We selected cohesin because it is a relatively well-studied SMC complex that is loaded at enhancer-promoter loops and can thus identify those interactions and can also migrate to CTCF sites and thus identify those interactions as well Kagey et al., 2010; Parelho et al., 2008; Rubio et al., 2008; Schaaf et al., 2013; Wendt et al., 2008).

The ChIA-PET technique was used because it yields high-resolution (˜4 kb) genome-wide interaction data, which is important because most loops involved in transcriptional regulation are between 1 and 100 kb (Gibcus and Dekker, 2013). We hoped to extend previous findings that mapped interactions among regulatory elements across portions of the ESC genome (Denholtz et al., 2013; Phillips-Cremins et al., 2013; Seitan et al., 2013) and gain a detailed understanding of the relationship between transcriptional control of ESC identity genes and control of local chromosome structure. To identify interactions between cohesin-occupied sites, we generated biological replicates of SMC1 ChIA-PET data sets in ESCs totaling ˜400 million reads (Table S1A). The two biological replicates showed a high degree of correlation (Pearson's r>0.91, Figures S1C and S1D), so we pooled the replicate data and processed it using an established protocol (Li et al., 2010), with modifications described in the Extended Experimental Procedures (Figure S1 and Table S1A). The data set contained ˜19 million unique paired-end tags (PETs) that were used to identify PET peaks (FIG. 1C). Interactions between PET peaks were identified and filtered for length and significance (FIG. 1C, S1E, and S1F, Table S1B, and Extended Experimental Procedures). The analysis method produced 1,234,006 cohesin-associated DNA interactions (FIG. 1C and Table S1B). The vast majority (92%) of these interacting cohesin-occupied sites occurred at enhancers, promoters, and CTCF-binding sites, consistent with the known roles of cohesin at these regulatory elements (FIG. 1D).

Genomic data of any type are noisy, and our confidence in the interpretation of DNA interaction data is improved by identifying PETs that represent independent events in the sample and pass statistical significance tests. For this reason, we generated a high-confidence interaction data set (described in Extended Experimental Procedures) by requiring that at least three independent PETs support the identified interaction between two PET peaks. The high-confidence data set consisted of 23,835 interactions that were almost entirely intrachromosomal (99%) and included 2,921 enhancer-promoter interactions, 2,700 enhancer-enhancer interactions, and 7,841 interactions between non-enhancer, non-promoter CTCF sites (FIGS. 1C, 1D, S1G, and S2 and Table S1B). Unless stated otherwise, the high-confidence data set was used for further quantitative analysis. We used the interaction data sets to create a table of enhancer-promoter assignments for ESCs (Tables S2A-S2C).

We found that the interaction data supported 83% of superenhancer assignments to the proximal active gene and 87% of typical enhancer assignments to the proximal active gene (Tables S2B and S2C), with approximately half of the remainder assigned to the second most proximal gene. The interaction data most frequently assigned super-enhancers and typical enhancers to a single gene, with 76% of super-enhancers and 84% of typical enhancers showing evidence of interaction with a single gene. Prior studies have suggested that there can be more frequent interactions between enhancers and genes (Kieffer-Kwon et al., 2013; Sanyal et al., 2012; Shen et al., 2012); our high-confidence data are not saturating and do not address the upper limits of these interactions (Figure S1H and Extended Experimental Procedures).

The catalog of enhancer-promoter assignments provided by these interaction data should prove useful for future studies of the roles of ESC enhancers and their associated factors in control of specific target genes. The majority of cohesin ChIA-PET interactions did not cross the boundaries of previously defined TADs (Dixon et al., 2012; Filippova et al., 2014; Meuleman et al., 2013; Wen et al., 2009) (FIG. 2 and Table S3A). FIG. 2A shows a representative example of a TAD, in which the majority (96%) of interactions occur within the domain. As expected from previous studies, the TAD boundaries are enriched for cohesin and CTCF and thus cohesin ChIA-PET peaks (FIG. 2B). Genome-wide analysis shows that 88% of all interactions are contained within TADs (FIG. 2C) and are somewhat enriched near the boundaries of TADs (FIG. 2D). The majority of cohesin ChIA-PET interactions did not cross lamin-associated domains (LADs), which are associated with repression at the nuclear periphery, or LOCK domains, which are large regions of chromatin marked with histone H3K9 modifications (Table S3A) (Meuleman et al., 2013; Wen et al., 2009). These results are consistent with properties previously described for TAD, LAD, and LOCK domain structures.

Super-Enhancer Domain Structure

Super-enhancers drive expression of key cell identity genes and are densely occupied by the transcription apparatus and its cofactors, including cohesin (Dowen et al., 2013; Hnisz et al., 2013). Analysis of high-confidence cohesin ChIA-PET interaction data revealed a striking feature common to loci containing super-enhancers and their associated genes (FIG. 3). This feature consisted of a super-enhancer and its associated gene located within a loop connected by two interacting CTCF sites co-occupied by cohesin (FIGS. 3A, 3B, and S3A-S3J). The vast majority of ESC super-enhancers (84%) are contained within these structures, which we call super-enhancer domains (SDs) (FIG. 3B, Tables S4A and S4B, and Extended Experimental Procedures).

In contrast, only 48% of typical enhancers were found to occur within comparable loops between two CTCF sites. The 197 SDs average 106 kb and most frequently contain one or two genes (Tables S4A and S4C). It was evident that there were cohesin-associated interactions between individual enhancer elements (constituents) of super-enhancers as well as interactions between super-enhancers and the promoters of their associated genes (Figures S3A-S3J).

Indeed, the results suggest that super-enhancer constituents have cohesin-associated interactions with one another (345 interactions) even more frequently than they do with their associated genes (216 interactions). The SDs contain high densities of pluripotency transcription factors, Mediator, and cohesin, together with histone modifications associated with transcriptionally active enhancers and genes (FIG. 3C). It was notable that the majority (82%) of interactions within SDs do not cross the CTCF sites at SD borders (FIG. 3D) and that the majority of Mediator, Pol2, and H3K27ac signal associated with super-enhancers and their associated genes occurs inside of the CTCF sites at SD borders (FIG. 3E).

The cohesin ChIA-PET interaction data and the distribution of the transcription apparatus suggest that the interacting cohesin-occupied CTCF sites tend to restrict the interactions of super-enhancers to those genes within the SD.

Super-Enhancer Domain Function

Because super-enhancers contain an exceptional amount of transcription apparatus and CTCF has been associated with insulator activity (Essafi et al., 2011; Handoko et al., 2011; Ong and Corces, 2014; Phillips and Corces, 2009; Phillips-Cremins and Corces, 2013), we postulated that SD structures might be necessary for proper regulation of genes in the vicinity of these structures. To test this model, we investigated the effect of deleting SD boundary CTCF sites on expression of genes inside and immediately outside of SDs (FIG. 4).

For this purpose, we studied five SDs whose super-enhancer-associated genes play key roles in embryonic stem cell biology (miR-290-295, Nanog, Tdgf1, Pou5f1 [Oct4], and Prdm14). In all cases, we found that deletion of a CTCF site led to altered expression of nearby genes. In four out of five cases, deletion of a CTCF site led to increased expression of genes immediately outside the SDs, and in three of five cases, deletion of a CTCF site caused changes in expression of genes within the SDs. The miR-290-295 locus, which specifies miRNAs with roles in ESC biology, is located within an SD (FIG. 4A). The miR-290-295 SD contains no other annotated gene, and the closest gene that resides outside this SD is Nlrp12, located ˜20 kb downstream of miR-290-295. CRISPR-mediated deletion of a boundary CTCF site (C1) at the miR-290-295 locus caused an ˜50% reduction in the miR-290-295 pri-miRNA transcript and an 8-fold increase in transcript levels for Nlrp12 (FIG. 4A). The CTCF deletion had no effect on expression of two genes located further away, AU018091 and Myadm (FIG. 4A).

These results indicate that normal expression of the miR-290-295 primiRNA transcript is dependent on the CTCF boundary site and furthermore that genes located immediately outside of this SD can be activated when the SD CTCF boundary site is disrupted. The Nanog gene, which encodes a key pluripotency transcription factor, is located within an SD shown in FIG. 4B. The Nanog SD contains no other annotated gene, and the closest upstream gene that resides outside this SD is Dppa3, which is located ˜50 kb upstream of Nanog.

CRISPR-mediated deletion of the boundary CTCF site C1 of the Nanog SD led to a ˜40% drop in Nanog transcript levels (FIG. 4B). In this case, there was no significant change in the level of the Dppa3 transcript (FIG. 4B). These results indicate that normal expression of the Nanog transcript is dependent on the C1 CTCF site. The Tdgf1 gene, which encodes an epidermal growth factor essential for embryonic development, is located within an SD (FIG. 4C). In this SD, it is possible that the super-enhancer regulates both the Tdgf1 and Lrrc2 genes and this Tdgf1/Lrrc2 SD also contains the Rtp3 gene. The closest gene that resides outside this SD is Gm590, which is located 30 kb downstream of Tdgf1. CRISPR-mediated deletion of a boundary CTCF site (C1) of the Tdgf1/Lrrc2 SD had little effect on Tdgf1 and Rtp3 transcript levels but had a modest effect on Lrrc2 transcript levels and caused a nearly 10-fold increase in the levels of Gm590 transcripts (FIG. 4C). The Pou5f1 gene, which encodes the pluripotency transcription factor OCT4, is located within an SD (FIG. 4D). The Pou5f1 SD contains no other annotated gene.

We were not able to obtain a bi-allelic CRISPR-mediated deletion of a boundary CTCF site despite multiple attempts, but we did obtain a mono-allelic deletion of the boundary CTCF site C1 (FIG. 4D). This mono-allelic deletion had little effect on the levels of Pou5f1 transcripts but increased the levels of transcripts for H2-Q10, the gene closest to the deleted boundary, by ˜2.5-fold (FIG. 4D). Transcription of the gene closest to the uninterrupted boundary of the Pou5f1 SD, Tcf19, was unaffected by the C1 deletion. The Prdm14 gene, which encodes a pluripotency transcription factor, is located within an SD (FIG. 4E). The Prdm14 SD contains no other annotated gene, and the closest downstream gene that resides outside this SD is Slco5a1, which is located 100 kb downstream of Prdm14. The Prdm14 SD has two neighboring cohesin-associated CTCF sites at one boundary; CRISPR-mediated deletion of a single boundary CTCF site (C1) had no effect on expression of Prdm14 or Slco5a1, but deletion of both CTCF sites (C1 and C2) at that boundary caused an ˜4.5-fold increase in expression of Slco5a1 (FIG. 4E).

We tested whether the super-enhancers from disrupted SD structures show increased interaction frequencies with the newly activated genes outside the SD by using 3C. At two loci where loss of an SD boundary CTCF site led to significant activation of the gene outside the SD (miR-290-295 and Pou5f1), we performed quantitative 3C experiments to measure the contact frequency between the super-enhancers and the genes immediately outside of SDs in wild-type cells and in cells where the SD boundary CTCF site was deleted. In both cases, loss of the CTCF site led to an increase in the contact frequency between the super-enhancers and the genes immediately outside of SDs that were newly activated (Figures S4A and S4B).

We investigated whether altered SD boundaries that affect cell identity genes cause ESCs to express markers consistent with an altered cell state. Indeed, we found that ESCs lacking the miR-290-295 boundary CTCF site C1 exhibit increased expression of the ectodermal marker Pax6 and decreased expression of the endodermal lineage markers Gata6 and Sox17, suggesting that loss of the SD structure is sufficient to affect cell identity (Figure S4C). Previous studies have shown that miR-290-295 null ESCs show an increased propensity to differentiate into ectodermal lineages at the expense of endoderm (Kaspi et al., 2013). In summary, the loss of CTCF sites at the boundaries of SDs can cause a change in the level of transcripts for superenhancer-associated genes within the SD and frequently leads to activation of genes near these CTCF sites. These results indicate that the integrity of SDs is important for normal expression of genes located in the vicinity of the SD, which can include genes that are key to control of cell identity.

Polycomb Domains

Maintenance of the pluripotent ESC state requires that genes encoding lineage-specifying developmental regulators are repressed, and these repressed lineage-specifying genes are occupied by nucleosomal histones that carry the polycomb-associated mark H3K27me3 (Margueron and Reinberg, 2011; Young, 2011). The mechanisms responsible for maintaining the H3K27me3 mark across short spans of regulatory regions and promoters of repressed genes are not well understood, although CTCF sites have been implicated (Cuddapah et al., 2009; Schwartz et al., 2012; Van Bortle et al., 2012).

Analysis of the H3K27me3-marked genes revealed that they, like the super enhancer-associated genes, are typically located within a loop between two interacting CTCF sites co-occupied by cohesin (FIGS. 5A, 5B, and S5A-S5J and Table S5A). These polycomb domain (PD) structures share many features with the super enhancer domains. The majority (70%) (380/546) of polycomb-associated genes occur in PD structures. PDs average 112 kb and generally contain one or two genes (Table S5B). The PDs contain exceptionally high densities of the polycomb proteins EZH2 and SUZ12 and the associated histone modification H3K27me3 (FIG. 5C).

The majority (78%) of cohesin ChIAPET interactions originating in PDs occur within the PD boundaries (FIG. 5D). Furthermore, the polycomb mark H3K27me3 tends to be retained within the PD (FIG. 5E).

We postulated that the CTCF boundaries that form PD structures might be important for repression of the polycomb-marked genes within the PD and investigated the effect of deleting boundary CTCF sites on a PD containing Tcfap2e to test this idea (FIG. 5F). CRISPR-mediated deletion of one of the boundary CTCF sites (C1) of the Tcfap2e PD caused a 1.7-fold increase in transcript levels for Tcfap2e (p<0.05) and no significant change in transcript levels for nearby genes within or outside of the PD.

CRISPR-mediated deletion of the other boundary CTCF site (C2) caused a 4-fold increase in the expression of Tcfap2e (p<0.001) and had little effect on adjacent genes. These results suggest that the integrity of the CTCF boundaries of PDs is important for full repression of H3K27me3-occupied genes.

Insulated Neighborhoods in Multiple Cell Types

A previous study suggested that DNA loops mediated by cohesin and CTCF tend to be larger and more shared among multiple cell types than DNA loops associated with cohesin and Mediator, which represent enhancer-promoter interactions that may be cell type specific (Phillips-Cremins et al., 2013). This led us to postulate that: (1) the interacting CTCF structures of SDs and PDs may be common to multiple cell types and (2) the acquisition of super-enhancers and polycomb binding within these common domain structures will vary based on the gene expression program of the cell type (FIG. 6A).

To test this model, we compared the SDs identified in ESCs to comparable regions in neural precursor cells (NPCs) for which 5C interaction data was available for specific loci (Phillips-Cremins et al., 2013).

We found, for example, that the Nanog locus SD observed in ESCs with ChIA-PET data was also detected by 5C data in NPCs (FIG. 6B). In NPCs, the Nanog gene is not expressed, and no super-enhancers are formed at this locus (FIG. 6B). Similarly, there is evidence for a common structure involving CTCF sites bounding the Olig1/Olig2 locus in both ESCs and NPCs (FIG. 6B).

In this domain, the Olig1/Olig2 genes are not active and no super-enhancers are formed in ESCs, whereas there are three super-enhancers in NPCs, where these genes are highly expressed (FIGS. 6B and S6).

For regions where 5C interaction data in NPCs and ChIA-PET interaction data in ESCs could be compared, a total of 11 out of 32 interactions between CTCF sites identified in NPCs were supported by interaction data in ESCs (Table S3B), which is impressive given the sparsity of interaction data.

This supports the view that the interacting CTCF structures of ESC SDs may be common to multiple cell types. If the CTCF boundaries of ESC SDs and PDs are common to many cell types, we would expect that the binding of CTCF to the SD and PD boundary sites observed in ESCs will be conserved across multiple cell types.

To test this notion, we examined CTCF ChIP-seq peaks from 18 mouse cell types and determined how frequently CTCF binding occurred across these cell types (FIG. 6C). When all ESC CTCF ChIP-seq peaks were included in the analysis, we found that there was fairly even distribution of the data into bins representing one or more cell types (FIG. 6C). In contrast, CTCF peaks co-bound by cohesin, which included those at SD and PD borders, were observed more frequently in bins representing a larger fraction of the cell types (FIG. 6C). These results indicate that the CTCF boundary sites of ESC SDs and PDs are frequently occupied by CTCF in multiple cell types and, together with the analysis of interaction data for NPCs described above, support the idea that CTCFCTCF interaction structures may often be shared by ESCs and more differentiated cell types.

TABLES

The following Tables are referenced throughout the specification.

TABLE S1A ChIA-PET linker sequences and mapping statistics Name Sequence Linker A 3′-GAC GAC AGG CTA T(biotin) AG CGC CGG-5′ 5′-CTG CTG TCC GAT ATC GC-3′ Linker B 3′-GAC GAC AGT ATA T(biotin) AG CGC CGG-5′ 5′-CTG CTG TCA TAT ATC GC-3′ mESC Smc1 Biological Biological ChIA-PET replicate 1 replicate 2 Total reads 221,653,525 176,705,499 chimeric 16,137,370  7% 10,348,925  6% non_chimeric 49,993,038 23% 58,657,541 33% too short 81,501,625 37% 80,181,174 45% (<27 nt after trimming) ambiguous 74,021,492 33% 27,517,859 16% PET1 PET2 PET1 PET2 Trimmed 49,993,038  49,993,038 58,657,541  58,657,541 Total aligned 36,439,501  36,149,180 42,213,793  41,932,150 Joined Mate  28,988,477  32,284,454 Pairs Unique Intra-   7,025,799   3,418,723 chromosomal Mate Pairs Unique Inter-   4,349,407   4,648,962 chromosomal Mate Pairs Ligations Intra-   1,239,023     980,462 chromosomal (>4 kb) Interactions Interactions      22,025      17,540 (PET2, FDR <0.01) Intra-      21,630      17,086 chromosomal Interactions Inter-         395         454 chromosomal Interactions chimeric _ Trimmed 16,137,370  16,137,370 10,348,925  10,348,925 Total aligned 11,597,024  11,438,519 7,443,723   7,380,674 Joined Mate   8,322,581   5,309,975 Pairs Unique Intra-     188,501      70,398 chromosomal Mate Pairs Unique Inter-   2,901,591   1,167,445 chromosomal Mate Pairs

TABLE S1B Frequencies of PETs and interactions at various thresholds Low Confidence High Confidence Unique Intra- and inter- Intra-chromosomal intra- chromosomal Interactions chromosomal Interactions (>4 kb, 3 PETs (>4 kb) PET, FDR 0.01) Total 10,444,522 1,234,006 23,739 Enhancer- 147,270 148,080 2,921 Promoter Enhancer- 2,252,066 104,394 2,700 Enhancer CTCF-CTCF 2,306,128 262,149 7,841 Inter-chromosomal Intra-chromosomal Inter:Intra Ratio 1 PETs 1,006,202 227,804 4:1  3+ PETs 96 23,739 1:247 Overlap with SMC1 ChIP- High Confidence seq peaks Interactions (>4 kb, 3 % of High confidence (1e−05) PET, FDR 0.01) Interactions Both End 21195 89.3% 1 End 2456 10.3% None 88 0.4%

TABLE S2B Super-enhancer to gene assignments Proximal active genes Interacting genes (SE within (SMC1 PET Nearest Chr Start End SE_ID SE_rank 4 kb of TSS) interactions) active genes chr1 36070190 36074608 INT_STITCHED_100 215 . Hs6st1 Hs6st1 chr1 36111164 36118698 INT_STITCHED_101 152 . Hs6st1 Hs6st1 chr1 72260528 72261272 INT_STITCHED_230 189 Mreg . Mreg chr1 72839563 72858199 INT_STITCHED_237 99 . Igfbp2 Igfbp2 chr1 91766947 91773527 INT_STITCHED_315 231 . Gbx2 Gbx2 chr1 120538712 120545414 INT_STITCHED_368 96 . Tcfcp2l1 Tcfcp2l1 chr1 120971968 120973737 INT_STITCHED_372 73 . Gli2 Gli2 chr1 121201424 121202481 INT_STITCHED_374 170 . Inhbb Inhbb chr1 121295085 121296031 INT_STITCHED_376 137 . Inhbb Inhbb chr1 138841643 138850970 INT_STITCHED_466 156 Nr5a2 Nr5a2 Nr5a2 chr1 168054897 168073079 INT_STITCHED_556 97 Dusp27, Gpa33 . Dusp27 chr1 169201106 169220423 INT_STITCHED_559 190 Uck2 . Uck2 chr1 182818684 182819554 INT_STITCHED_610 59 Lefty2 . Lefty2 chr1 182854521 182864307 INT_STITCHED_611 54 Lefty1 Lefty2, Lefty1 Tmem63a, Lefty1 chr1 183948212 183961841 INT_STITCHED_615 123 Enah . Enah chr2 20574602 20591747 INT_STITCHED_746 25 . Etl4 Etl4 chr2 32008891 32030736 INT_STITCHED_812 31 Bat2l . Bat2l chr2 33282029 33300860 INT_STITCHED_817 56 Zbtb34 Zbtb34 Zbtb34 chr2 71488013 71494617 INT_STITCHED_928 115 . Gm1631 Gm1631 chr2 152552277 152563676 INT_STITCHED_1198 178 Id1 Id1 Id1 chr2 162877048 162893236 INT_STITCHED_1257 18 Mybl2 . Mybl2 chr2 165981373 165983444 INT_STITCHED_1279 121 Sulf2 . Sulf2 chr2 168589688 168617170 INT_STITCHED_1300 95 Sall4 . Sall4 chr3 34544904 34553511 INT_STITCHED_1480 34 Sox2 Mir1897 Sox2 chr3 34633687 34660705 INT_STITCHED_1482 2 . Mir1897, Sox2 Sox2 chr3 88375442 88380083 INT_STITCHED_1607 193 Ssr2 . Ssr2 chr3 95455034 95468269 INT_STITCHED_1626 9 Mcl1 . Mcl1 chr3 96380383 96382115 INT_STITCHED_1629 69 . Txnip, Txnip Ankrd34a, Polr3gl chr3 96479158 96484864 INT_STITCHED_1630 116 Ankrd35 Ankrd35, Ankrd35 Nudt17 chr3 129247012 129261362 INT_STITCHED_1732 112 . Elovl6 Elovl6 chr4 118743867 118745786 INT_STITCHED_2152 23 . Slc2a1 Slc2a1 chr4 125211671 125223450 INT_STITCHED_2192 143 . Grik3 Grik3 chr4 137329436 137357766 INT_STITCHED_2268 108 Alpl Alpl Alpl chr4 138000554 138006368 INT_STITCHED_2273 228 Camk2n1 Camk2n1 Camk2n1 chr4 141120768 141126477 INT_STITCHED_2292 39 . Gm694, B330016D10Rik B330016D10Rik, Fblim1, Tmem82, AI507597 chr4 147459254 147463850 INT_STITCHED_2317 196 Agtrap . Agtrap chr5 53933177 53947327 INT_STITCHED_2510 71 Rbpj . Rbpj chr5 65255735 65256794 INT_STITCHED_2535 84 . Klf3 Klf3 chr5 113758941 113775389 INT_STITCHED_2712 64 Mir469 Mir469 Mir469 chr5 116845764 116860853 INT_STITCHED_2736 153 . Hspb8, Hspb8 2410137F16Rik chr5 118884660 118896412 INT_STITCHED_2745 35 . Med13l Med13l chr5 123584659 123590728 INT_STITCHED_2770 41 Rhof Rhof Rhof chr5 135417523 135421698 INT_STITCHED_2830 142 Cldn4 . Cldn4 chr6 39370384 39371286 INT_STITCHED_3044 225 Mkrn1 . Mkrn1 chr6 91640161 91661247 INT_STITCHED_3217 124 Slc6a6 Slc6a6 Slc6a6 chr6 122290093 122293017 INT_STITCHED_3342 13 Phc1 . Phc1 chr6 122640118 122657871 INT_STITCHED_3348 32 Nanog, Nanog, Nanog Nanogpd Nanogpd chr6 122714316 122720862 INT_STITCHED_3349 40 . Slc2a3 Slc2a3 chr6 142458188 142461905 INT_STITCHED_3429 222 Ldhb . Ldhb chr6 143047309 143065758 INT_STITCHED_3437 98 5730419I09Rik . 5730419I09Rik chr6 145223385 145225674 INT_STITCHED_3450 230 . Kras Kras chr7 3193004 3218183 INT_STITCHED_3467 1 LOC100303645, LOC100303645, LOC100303645 Mir291b, Mir291b, Mir293, Mir293, Mir290, Mir290, Mir291a, Mir291a, Mir292, Mir292, Mir294, Mir294, Mir295 Mir295 chr7 13599334 13600325 INT_STITCHED_3481 172 Zbtb45 Zbtb45, Zbtb45 Trim28 chr7 30982397 30983339 INT_STITCHED_3523 154 Capns1 Cox7a1 Capns1 chr7 31248315 31250619 INT_STITCHED_3525 87 Nphs1 Aplp1, Nphs1 Nphs1, Kirrel2 chr7 52806853 52814768 INT_STITCHED_3568 201 . Bcat2 Bcat2 chr7 71092246 71102481 INT_STITCHED_3601 102 . Klf13 Klf13 chr7 87159908 87169963 INT_STITCHED_3658 176 Zfp710 . Zfp710 chr7 87274999 87276022 INT_STITCHED_3661 65 . Idh2 Idh2 chr7 87333420 87345334 INT_STITCHED_3662 209 Sema4b Sema4b Sema4b chr7 91027196 91051830 INT_STITCHED_3685 199 Mesdc1, Mesdc2 . Mesdc1 chr7 119831735 119835688 INT_STITCIIED_3765 166 . Tead1 Tead1 chr7 140304156 140307245 INT_STITCHED_3856 51 . Ctbp2 Ctbp2 chr8 12499468 12504771 INT_STITCHED_3947 125 . Sox1 Sox1 chr8 35023426 35027483 INT_STITCHED_4014 173 . Rbpms Rbpms chr8 37602064 37613850 INT_STITCHED_4033 6 . Dlc1 Dlc1 chr8 37642521 37671979 INT_STITCHED_4034 36 . Dlc1 Dlc1 chr8 44405736 44406755 INT_STITCHED_4046 161 . Zfp42 Zfp42 chr8 87174072 87174643 INT_STITCHED_4163 79 . Ier2 Ier2 chr8 91514813 91540176 INT_STITCHED_4179 15 . Sall1 Sall1 chr8 93351924 93355292 INT_STITCHED_4190 131 Chd9 . Chd9 chr9 78207143 78223442 INT_STITCHED_4657 14 Ooep, Dppa5a Dppa5a, Ooep Dppa5a chr9 110849422 110863371 INT_STITCHED_4748 4 Lrrc2 Tdgf1, Lrrc2 Lrrc2 chr9 114458126 114474355 INT_STITCHED_4766 113 Trim71 Trim71 Trim71 chr10 21546502 21549691 INT_STITCHED_4891 135 . Sgk1 Sgk1 chr10 21700576 21708946 INT_STITCHED_4893 68 Sgk1 Sgk1 Sgk1 chr10 39977900 39978752 INT_STITCHED_4495 60 Gtf3c6 . Gtf3c6 chr10 59420365 59437537 INT_STITCHED_5021 181 Ddit4 Ddit4 Ddit4 chr10 62346394 62361563 INT_STITCHED_5044 5 Tet1 . Tet1 chr10 66380351 66383761 INT_STITCHED_5054 164 . Reep3 Reep3 chr10 66546199 66564235 INT_STITCHED_5059 134 Reep3 Reep3 Reep3 chr10 75400370 75401358 INT_STITCHED_5092 183 Mmpl1, Mmpl1, Chchd10 Chchd10 Chchd10, Vpreb3, Gm5134 chr10 76655655 76662360 INT_STITCHED_5100 187 . Col18a1 Col18a1 chr10 79508474 79515168 INT_STITCHED_5111 55 Polr2e, Gpx4 Gpx4 Gpx4 chr11 52173182 52184686 INT_STITCHED_5484 218 Vdac1 Vdac1 Vdac1 chr11 66824791 66838230 INT_STITCHED_5555 74 Tmem220 Pirt, Tmem220, Tmem220 Myh3 chr11 77697704 77718786 INT_STITCHED_5597 58 Pipox Pipox Pipox chr11 97517673 97524159 INT_STITCHED_5711 24 . Pcgf2, Mllt6, Cisd3 Cisd3 chr11 98823511 98826466 INT_STITCHED_5719 194 Rara Rara Rara chr11 116943025 116953583 INT_STITCHED_5819 57 2810008D09Rik Sec14l1 2810008D09Rik chr12 12790432 12795881 INT_STITCHED_5875 38 . Mycn Mycn chr12 12810177 12811020 INT_STITCHED_5876 185 . Mycn Mycn chr12 12933791 12950936 INT_STITCHED_5880 45 Mycn Mycn Mycn chr12 56587347 56607146 INT_STITCHED_6000 165 Nfkbia Nfkbia Nfkbia chr12 88239069 88245155 INT_STITCHED_6118 90 . 6430527G18Rik, 2310044G17Rik 2310044G17Rik chr12 103940487 103953004 INT_STITCHED_6151 197 Itpk1 . Itpk1 chr12 111725920 111743677 INT_STITCHED_6188 117 Ppp2r5c . Ppp2r5c chr13 98052562 98062842 INT_STITCHED_6557 217 . Enc1 Enc1 chr13 98202400 98225162 INT_STITCHED_6559 182 . Enc1 Enc1 chr14 55704349 55705463 INT_STITCHED_6815 145 Zfhx2 Jph4, Zfhx2, Zfhx2 Thtpa chr14 64118817 64131901 INT_STITCHED_6859 62 Tdh Tdh Tdh chr14 65251303 65269514 INT_STITCHED_6864 219 Kif13b Kif13b Kifl3b chr14 71022659 71035930 INT_STITCHED_6887 66 Fgf17 Fgf17 Fgf17 chr14 76894682 76915946 INT_STITCHED_6904 27 Tsc22d1 Tsc22d1 Tsc22d1 chr14 106250319 106260753 INT_STITCHED_6981 140 . Spry2 Spry2 chr14 106296486 106304433 INT_STITCHED_6982 110 Spry2 . Spry2 chr16 23099373 23103471 INT_STITCHED_7434 101 Eif4a2, Snord2 . Eif4a2 chr16 84769173 84780686 INT_STITCHED_7597 53 Jam2 Mrp139, Jam2 Jam2 chr17 10549089 10570838 INT_STITCHED_7680 114 . Qk Qk chr17 26631721 26648689 INT_STITCHED_7728 139 Dusp1 Dusp1 Dusp1 chr17 29209618 29218426 INT_STITCHED_7747 200 . Cdkn1a Cdkn1a chr17 29587776 29588942 INT_STITCHED_7752 157 . Pim1 Pim1 chr17 31939569 31956756 INT_STITCHED_7767 29 . Sik1 Sik1 chr17 35639211 35642435 INT_STITCHED_7784 186 Pou5f1 Tcf19, Cchcr1 Pou5f1 chr17 37110202 37134996 INT_STITCHED_7792 12 2410137M14Rik, Znrd1, Znrd1as, 2410137M14Rik Zfp57, 2410137M14Rik, H2-M5 Trim40, Gabbr1, H2-M5, Zfp57, Olfr90 chr17 45593477 45596503 INT_STITCHED_7812 37 . Spats1 Spats1 chr17 47640414 47649043 INT_STITCHED_7822 141 Ccnd3, Taf8 Ccnd3, Bysl, Ccnd3 Med20 chr17 71213804 71222433 INT_STITCHED_7887 42 . Tgif1 Tgif1 chr17 71241991 71250610 INT_STITCHED_7888 203 . Tgif1 Tgif1 chr18 75504155 75505202 INT_STITCHED_8260 198 . Smad7 Smad7 chr18 75520332 75527277 INT_STITCHED_8261 91 Smad7 Smad7 Smad7 chr19 5835881 5847014 INT_STITCHED_8324 16 Neat1 Malat1, Neat1 Slc25a45, Frmd8 chr19 21858770 21866770 INT_STITCHED_8378 103 Tmem2 Tmem2 Tmem2 chr19 23207455 23208806 INT_STITCHED_8386 82 . Klf9,Mir1192 Klf9 chrX 50098631 50114110 INT_STITCHED_8629 150 Mir18b, . Kis2 Mir19b-2, Kis2, Mir20b, Mir92-2, Mir106a, Mir363

TABLE S2C Typical enhancer to gene assignment proximal interacting active genes active genes (TE within (SMC1 PET nearest chr start end TE_ID TE_rank 4 kb of TSS) interactions) genes chr1 4845264 4846195 INT_STITCHED_4 4358 Tcea1 . Tcea1 chr1 9691815 9692699 INT_STITCHED_22 2543 Mybl1 . Mybl1 chr1 10021675 10022274 INT_STITCHED_25 4284 Csppl, Cops5 . Cops5 chr1 12681792 12682608 INT_STITCHED_40 2368 Sulf1 . Sulf1 chr1 12734270 12735431 INT_STITCHED_41 521 . Sulf1 Sulf1 chr1 13650476 13651156 INT_STITCHED_48 726 Lactb2 . Lactb2 chr1 14302611 14303160 INT_STITCHED_54 5331 Eya1 . Eya1 chr1 20944720 20945563 INT_STITCHED_66 3579 Efhc1 . Efhc1 chr1 34063557 34064527 INT_STITCHED_87 1218 Dst . Dst chr1 36296870 36297624 INT_STITCHED_102 4246 Uggt1 . Uggt1 chr1 38960832 38961217 INT_STITCHED_122 5874 Chst10 . Chst10 chr1 39959153 39960298 INT_STITCHED_127 3253 Map4k4 . Map4k4 chr1 52065557 52066452 INT_STITCHED_153 3287 Stat4 . Stat4 chr1 53009978 53010966 INT_STITCHED_156 499 1700019D03Rik . 1700019D03Rik chr1 55188460 55189193 INT_STITCHED_165 3945 Mobkl3 . Mobkl3 chr1 58045669 58046468 INT_STITCHED_177 7085 Sgol2 . Sgol2 chr1 59543982 59544804 INT_STITCHED_185 1108 Fzd7 . Fzd7 chr1 63256644 63260998 INT_STITCHED_199 729 Gpr1 . Gpr1 chr1 63488535 63489242 INT_STITCHED_201 2410 Adam23 . Adam23 chr1 66746373 66747073 INT_STITCHED_217 2899 Rpe . Rpe chr1 71692414 71697825 INT_STITCHED_227 505 Fn1 Fn1 Fn1 chr1 71719790 71720485 INT_STITCHED_228 1904 . Fn1 Fn1 chr1 72359403 72360070 INT_STITCHED_234 1813 Xrcc5 . Xrcc5 chr1 72873970 72875037 INT_STITCHED_238 905 Igfbp2 . Igfbp2 chr1 74354703 74355378 INT_STITCHED_245 5971 Tmbim1 . Tmbim1 chr1 75477134 75477769 INT_STITCHED_250 5588 Chpf, Tmem198 . Chpf chr1 75508284 75508949 INT_STITCHED_251 1914 Obsl1, Inha . Inha chr1 82816971 82817766 INT_STITCHED_274 2678 . Agfg1 Agfg1 chr1 87920884 87921540 INT_STITCHED_284 3696 Spata3 . Spata3 chr1 87959141 87959957 INT_STITCHED_285 4733 Psmd1 . Psmd1 chr1 88204615 88208596 INT_STITCHED_290 250 B3gnt7 B3gnt7 B3gnt7 chr1 88245025 88246107 INT_STITCHED_291 2122 Snora75 . Snora75 chr1 90565168 90566043 INT_STITCHED_305 2089 . Arl4c Arl4c chr1 91819328 91831892 INT_STITCHED_316 497 Gbx2 Gbx2 Gbx2 chr1 92098794 92106028 INT_STITCHED_318 688 Cxcr7 . Cxcr7 chr1 95376908 95377612 INT_STITCHED_332 6388 Hdlbp, Sept2 . Hdlbp chr1 98771158 98773296 INT_STITCHED_339 2005 Slco4c1 . Slco4c1 chr1 99983100 99989373 INT_STITCHED_342 3966 Pam . Pam chr1 108073359 108073939 INT_STITCHED_358 8767 Phlpp1 . Phlppl chr1 120521806 120522612 INT_STITCHED_367 2301 Tcfcp2l1 . Tcfcp2l1 chr1 120945487 120946330 INT_STITCHED_371 1302 Gli2 . Gli2 chr1 121974196 121974786 INT_STITCHED_381 3822 Tmem37 . Tmem37 chr1 133035565 133036620 INT_STITCHED_412 1146 Dyrk3 . Dyrk3 chr1 133808795 133809368 INT_STITCHED_417 5138 Nucks1 . Nucks1 chr1 134094126 134098050 INT_STITCHED_418 325 Mir135b, . Mir135b Lemd1 chr1 134219166 134219919 INT_STITCHED_422 1727 Nuak2 . Nuak2 chr1 134367243 134368398 INT_STITCHED_423 926 Rbbp5 . Rbbp5 chr1 134632637 134633301 INT_STITCHED_424 7437 Nfasc . Nfasc chr1 134908975 134916403 INT_STITCHED_428 576 Mdm4 . Mdm4 chr1 135025718 135027101 INT_STITCHED_430 1307 Ppp1r15b . Ppp1r15b chr1 135293890 135294788 INT_STITCHED_433 1273 . Sox13 Sox13 chr1 135388767 135401699 INT_STITCHED_434 543 . Sox13 Sox13 chr1 135563926 135569034 INT_STITCHED_435 358 Zc3h11a, . Zc3h11a Zbed6 chr1 135590624 135593014 INT_STITCHED_436 560 Lax1 . Lax1 chr1 136397332 136398015 INT_STITCHED_443 4773 Rabif . Rabif chr1 136431225 136432331 INT_STITCHED_444 2150 . Kdm5b Kdm5b chr1 137113999 137114858 INT_STITCHED_450 706 . Elf3 Elf3 chr1 137620382 137621364 INT_STITCHED_456 2681 Csrp1 . Csrp1 chr1 145580899 145581539 INT_STITCHED_484 4234 Glrx2 . Glrx2 chr1 153273953 153274850 INT_STITCHED_494 8758 1200016B10Rik, . 1200016B10Rik 1190005F20Rik chr1 154747403 154748240 INT_STITCHED_504 3069 Smg7 . Smg7 chr1 155038686 155047086 INT_STITCHED_509 1743 Lamc2 . Lamc2 chr1 155587804 155588362 INT_STITCHED_515 8754 Rgs16 . Rgs16 chr1 158404784 158405439 INT_STITCHED_524 5448 Soat1 . Soat1 chr1 158598688 158600322 INT_STITCHED_526 564 Tor3a Tor3a Tor3a chr1 159347974 159348711 INT_STITCHED_530 5728 Rasal2, . Rasal2 2810025M15Rik chr1 162139563 162148759 INT_STITCHED_536 836 Cacybp Mrps14 Cacybp chr1 163177529 163178269 INT_STITCHED_540 5753 Prdx6 . Prdx6 chr1 166391111 166401507 INT_STITCHED_550 1257 Atp1b1 . Atp1b1 chr1 166420037 166434276 INT_STITCHED_551 257 . Atp1b1 Atp1b1 chr1 167932859 167934026 INT_STITCHED_555 955 Pou2f1 . Pou2f1 chr1 170356969 170357484 INT_STITCHED_564 6866 Pbx1 . Pbx1 chr1 172801604 172802054 INT_STITCHED_569 2160 Atf6 . Atf6 chr1 173151620 173152144 INT_STITCHED_573 1593 Apoa2, 1700009P17Rik Tomm401 Tomm401 chr1 173954295 173954872 INT_STITCHED_575 7014 Vangl2 . Vangl2 chr1 174253188 174253931 INT_STITCHED_577 8046 Kcnj9 . Kcnj9 chr1 180267618 180268830 INT_STITCHED_593 731 Hnrnpu . Hnrnpu chr1 180336631 180337473 INT_STITCHED_594 2688 Efcab2 . Efcab2 chr1 182500935 182501845 INT_STITCHED_609 1729 Parp1 . Parp1 chr1 187032263 187033005 INT_STITCHED_625 4425 Rab3gap2 . Rab3gap2 chr1 187934331 187934769 INT_STITCHED_630 7896 Lyplal1 . Lyplal1 chr1 190822409 190837835 INT_STITCHED_646 676 Kctd3 . Kctd3 chr1 191740124 191740887 INT_STITCHED_650 1458 Smyd2 . Smyd2 chr1 192888978 192894651 INT_STITCHED_655 2500 Tatdn3, Nsl1 . Tatdn3 chr1 193647966 193643573 INT_STITCHED_660 6749 Nek7 . Nek2 chr1 194590595 194591390 INT_STITCHED_664 6035 Hhat . Hhat chr1 195330571 1953334 INT_STITCHED_670 2128 Mir205 . Mir205 chr1 196442242 196442858 INT_STITCHED_676 7610 Plxna2 . Plxna2 chr2 17854471 17865277 INT_STITCHED_732 482 . LOC100034739 LOC100034739 chr2 17895135 17911418 INT_STITCHED_733 361 . LOC100034739 LOC100034739 chr2 22747132 22756399 INT_STITCHED_756 797 Pdss1 . Pdss1 chr2 26198387 26199182 INT_STITCHED_766 5022 . Dnlz Dnlz chr2 26298047 26304190 INT_STITCHED_767 2561 Sec16a Notch1 Sec16a chr2 26356857 26358299 INT_STITCHED_768 1708 Notch1 . Notch1 chr2 28361728 28365199 INT_STITCHED_775 3084 Ralgds . Ralgds chr2 28391046 28391512 INT_STITCHED_776 6931 Ralgds . Ralgds chr2 28976424 28976978 INT_STITCHED_783 3537 Setx . Setx chr2 29100520 29101142 INT_STITCHED_785 2171 Ntng2 . Ntng2 chr2 29484671 79487572 INT_STITCHED_790 375 . Rapgef1 Rapgef1 chr2 29675439 29676619 INT_STITCHED_793 1058 Urm1 . Urm1 chr2 29917303 29917729 INT_STITCHED_796 1358 Set . Set chr2 29990414 29991153 INT_STITCHED_797 2134 Tbcld13 . Tbcld13 chr2 31427293 31428087 INT_STITCHED_808 635 Fubp3 Prdm12 Fubp3 chr2 31736153 31736754 INT_STITCHED_810 5015 Lamc3 . Lamc3 chr2 33738008 33739000 INT_STITCHED_823 4826 Fam125b . Fam125b chr2 38780488 38781118 INT_STITCHED_839 3934 Olfml2a, Wdr38 Nr6a1 Nr6a1 chr2 44959885 44960550 INT_STITCHED_849 4033 Gm13476 . Gm13476 chr2 49304139 49305084 INT_STITCHED_856 7363 Epc2 . Epc2 chr2 50894125 50905941 INT_STITCHED_861 897 . Rnd3 Rnd3 chr2 51926608 51928267 INT_STITCHED_865 280 Rif1 . Rif1 chr2 60213132 60223107 INT_STITCHED_884 419 Ly75 . Ly75 chr2 62246033 62246887 INT_STITCHED_895 3985 Dpp4 . Dpp4 chr2 65679605 65687302 INT_STITCHED_900 745 Csmp3 . Csrnp3 chr2 71556963 71557704 INT_STITCHED_930 400 Gm1631 . Gm1631 chr2 71704256 71705255 INT_STITCHED_932 380 Pdk1 Pdk1 Pdk1 chr2 72823322 72824095 INT_STITCHED_936 3178 Sp3 . Sp3 chr2 75544463 75545103 INT_STITCHED_951 2667 Nfe2l2 . Nfe2l2 chr2 76238133 76238918 INT_STITCHED_958 3707 Osbp16 . Osbp16 chr2 79269600 79270299 INT_STITCHED_973 2411 Cerkl Neurod1 Cerkl chr2 83550377 83559168 INT_STITCHED_980 1203 Itgav . Itgav chr2 84677181 84679035 INT_STITCHED_986 860 Slc43a1 . Slc43a1 chr2 91544344 91548597 INT_STITCHED_993 3127 Atg13, . Atg13 Harbi1 chr2 91772530 91773198 INT_STITCHED_994 1226 Mdk Chrm4 Mdk chr2 94103254 94103817 INT_STITCHED_1002 2880 Mir670 . Mir670 chr2 102023859 102024282 INT_STITCHED_1013 6628 Ldlrad3 . Ldlrad3 chr2 102243909 102243994 INT_STITCHED_1014 8718 Trim44 . Trim44 chr2 103632070 103632867 INT_STITCHED_1022 3964 Caprin1 . Caprin1 chr2 103938892 103939697 INT_STITCHED_1024 4914 Cd59a . Cd59a chr2 104428555 104429275 INT_STITCHED_1026 6129 Cstf3 . Cstf3 chr2 104657804 104666793 INT_STITCHED_1028 1623 Qser1 . Qser1 chr2 104695622 104696627 INT_STITCHED_1029 3340 Prrg4 . Prrg4 chr2 105237758 105249007 INT_STITCHED_1031 1507 Rcn1 . Rcn1 chr2 109753059 109753825 INT_STITCHED_1048 2198 Gm13939, . Gm13939 Lgr4 chr2 114003762 114004516 INT_STITCHED_1054 2091 Aqr . Aqr chr2 115885482 115886413 INT_STITCHED_1061 3063 Meis2 3110099E03Rik, Meis2 2810405F15Rik chr2 116945256 116946216 INT_STITCHED_1066 1301 Spred1 . Spred1 chr2 119615493 119616460 INT_STITCHED_1079 1269 Rpap1 Tyro3 Rpap1 chr2 120069560 120070347 INT_STITCHED_1081 4738 Pla2g4e . Pla2g4e chr2 121095895 121096949 INT_STITCHED_1083 5489 Trp53bp1 . Trp53bp1 chr2 121303040 121303595 INT_STITCHED_1084 4080 Mfap1b . Mfap1b chr2 121628647 121629289 INT_STITCHED_1086 6300 Frmd5 . Frmd5 chr2 122195660 122196747 INT_STITCHED_1091 1739 Shf . Shf chr2 125973476 125973812 INT_STITCHED_1098 7151 Dtwdl . Dtwdl chr2 127664828 127665772 INT_STITCHED_1105 2730 . Bub1 Bub1 chr2 128638582 128639150 INT_STITCHED_1111 3886 Tmem87b . Tmem87b chr2 128887217 128888053 INT_STITCHED_1113 6432 Ttl . Ttl chr2 129412877 129414126 INT_STITCHED_1117 2016 Sirpa . Sirpa chr2 129521285 129528427 INT_STITCHED_1118 967 Pdyn . Pdyn chr2 129623870 129626180 INT_STITCHED_1119 1155 Stk35, . Stk35 4932416H05Rik chr2 131058146 131070063 INT_STITCHED_1125 1091 Mays . Mays chr2 140502439 140503025 INT_STITCHED_1155 3559 Flrt3 . Flrt3 chr2 145614651 145615227 INT_STITCHED_1167 5472 Rin2 . Rin2 chr2 146837021 146837769 INT_STITCHED_1177 2634 Xrn2 . Xrn2 chr2 148700392 148701063 INT_STITCHED_1185 1716 Cst3 9230104L09Rik Cst3 chr2 150482907 150491844 INT_STITCHED_1190 744 Acss1 . Acss1 chr2 150863293 150863974 INT_STITCHED_1193 7212 Nanp . Nanp chr2 152048814 152049781 INT_STITCHED_1197 4239 Csnk2a1 . Csnk2a1 chr2 152932871 152933554 INT_STITCHED_1200 1971 Hck . Hck chr2 153172351 153173278 INT_STITCHED_1202 2564 Asxl1 . Asxl1 chr2 153467302 153469325 INT_STITCHED_1208 3527 Dnmt3b . Dnmt3b chr2 154905247 154906205 INT_STITCHED_1212 5226 Ahcy . Ahcy chr2 156251118 156251931 INT_STITCHED_1218 1519 Epb4.1l1 . Epb4.1l1 chr2 156667667 156668409 INT_STITCHED_1223 1808 Tgif2 . Tgif2 chr2 157243952 157244973 INT_STITCHED_1229 337 Src Ghrh, Src Src chr2 157978463 157980974 INT_STITCHED_1233 239 Tgm2 . Tgm2 chr2 158614658 158615457 INT_STITCHED_1238 4450 Dhx35 . Dhx35 chr2 162753625 162754468 INT_STITCHED_1255 7920 Srsf6 . Srsf6 chr2 163890381 163891019 INT_STITCHED_1261 6983 Tomm34 . Tomm34 chr2 164277250 164277825 INT_STITCHED_1263 4381 . Sdc4 5dc4 chr2 164649260 164649880 INT_STITCHED_1265 1164 Zswim1, . Zswim1 1700020007Rik chr2 164680558 164681078 INT_STITCHED_1266 5540 Pltp . Pltp chr2 165682802 165683641 INT_STITCHED_1273 1421 . Zmynd8 Zmynd8 chr2 165700123 165704304 INT_STITCHED_1274 2229 Zmynd8 . Zmynd8 chr2 165719928 165725066 INT_STITCHED_1275 557 . Zmynd8 Zmynd8 chr2 166019666 166020678 INT_STITCHED_1280 431 . Sulf2 Sulf2 chr2 166884075 166898489 INT_STITCHED_1288 240 Snord12, Kcnb1 Snord12 1500012E01Rik, Znfx1 chr2 167248382 167249300 INT_STITCHED_1294 2679 Slc9a8 . Slc9a8 chr2 167355489 167366175 INT_STITCHED_1295 652 Snai1 . Snai1 chr2 167979755 167980437 INT_STITCHED_1297 1110 . Adnp Adnp chr2 168039253 168040134 INT_STITCHED_1299 6482 . Adnp Adnp chr2 168664093 168667592 INT_STITCHED_1301 675 . Atp9a, Sall4 Sall4 chr2 168784552 168785568 INT_STITCHED_1302 1060 Zfp64 . Zfp64 chr2 174082837 174087567 INT_STITCHED_1339 943 Mir296 . Mir296 chr2 174113130 174113943 INT_STITCHED_1340 2341 Gnas . Gnas chr2 180443435 180445072 INT_STITCHED_1358 534 Dido1, Slc17a9 Dido1 2310003C93Rik chr2 180462024 180475727 INT_STITCHED_1359 329 Slc17a9 Slc17a9, Slc17a9 Dido1 chr2 180687447 180688955 INT_STITCHED_1362 2111 Nkain4 Birc7, Arfgap1 Nkain4 chr2 180947699 180948243 INT_STITCHED_1364 3425 BC051628 Ppdpf BC051628 chr2 180979223 180980098 INT_STITCHED_1365 7507 BC006779 . BC006779 chr2 181056733 181067845 INT_STITCHED_1366 1346 Rtel1 . Rtel1 chr3 7366490 7367336 INT_STITCHED_1376 8686 Pkia . Pkia chr3 8509668 8511844 INT_STITCHED_1381 318 Stmn2 . Stmn2 chr3 8963969 8965013 INT_STITCHED_1382 3662 Tpd52 . Tpd52 chr3 9008384 9009250 INT_STITCHED_1384 1165 Tpd52 . Tpd52 chr3 9243943 9244611 INT_STITCHED_1386 4596 Zbtb10 . Zbtb10 chr3 9610853 9611748 INT_STITCHED_1391 1939 Zfp704 C030034L19Rik Zfp704 chr3 10353887 10354547 INT_STITCHED_1395 5545 Zfand1 . Zfand1 chr3 14863038 14863599 INT_STITCHED_1406 1714 Car3 . Car3 chr3 18523768 18524685 INT_STITCHED_1418 1649 . Cyp7b1 Cyp7b1 chr3 19797116 19797596 INT_STITCHED_1423 7359 4632415L05Rik . 4632415L05Rik chr3 19957995 19958715 INT_STITCHED_1425 3002 Hltf . Hltf chr3 21834336 21835378 INT_STITCHED_1430 708 . Tbl1xr1 Tbl1xr1 chr3 21964172 21975748 INT_STITCHED_1433 312 Tbl1xr1 . Tbl1xr1 chr3 27602172 27603039 INT_STITCHED_1447 1051 Fndc3b . Fndc3b chr3 27834469 27836247 INT_STITCHED_1449 2019 Pld1 . Pd1 chr3 30545417 30547747 INT_STITCHED_1462 694 Lrriq4 . Lrriq4 chr3 30899964 30917089 INT_STITCHED_1468 432 Prkci . Pkci chr3 30988014 30988781 INT_STITCHED_1469 1571 Skil . Skil chr3 53261382 53262179 INT_STITCHED_1518 2450 2810046L04Rik, . Nhlrc3 Nhlrc3 chr3 53453757 53454852 INT_STITCHED_1521 1227 Frem2 Frem2 Frem2 chr3 53672950 53673878 INT_STITCHED_1522 3451 Ufm1 . Ufm1 chr3 57536429 57536949 INT_STITCHED_1530 4492 Rnf13 . Rnf13 chr3 62145578 62146250 INT_STITCHED_1539 5028 4631416L12Rik . 4631416L12Rik chr3 63098862 63099542 INT_STITCHED_1541 2296 Mme . Mme chr3 65339039 65339696 INT_STITCHED_1548 7074 4931440P22Rik . 4931440P22Rik chr3 67307480 67318756 INT_STITCHED_1552 1308 Rarres1 . Rarres1 chr3 68368482 68369877 INT_STITCHED_1558 1231 Schip1 . Schipl chr3 79375842 79376337 INT_STITCHED_1573 6825 Fnip2 . Fnip2 chr3 80838336 80839401 INT_STITCHED_1575 1948 Pdgfc . Pdgfc chr3 83824381 83838289 INT_STITCHED_1586 957 D930015E06Rik . D930015E06Rik chr3 83985389 84010994 INT_STITCHED_1587 439 . Gm6525, Gm6525 Trim2 chr3 84624646 84625298 INT_STITCHED_1589 7481 Fbxw7 . Fbxw7 chr3 85952913 85953587 INT_STITCHED_1596 4519 Rps3a . Rps3a chr3 86940621 86941199 INT_STITCHED_1600 3865 . Kirrel Kirrel chr3 87777956 87778942 INT_STITCHED_1603 1687 Nes . Nes chr3 89258497 89259386 INT_STITCHED_1609 2576 Pmvk . Pmvk chr3 89626047 89631123 INT_STITCHED_1611 1463 She . She chr3 94110855 94111307 INT_STITCHED_1620 5187 Them4 . Them4 chr3 94965812 94966422 INT_STITCHED_1623 3377 Sema6c . Sema6c chr3 95237742 95238552 INT_STITCHED_1625 1341 Gm4349, . Arnt Arnt chr3 95505802 95506443 INT_STITCHED_1627 539 . Adamtsl4 Adamtsl4 chr3 95694960 95695228 INT_STITCHED_1628 3845 BC028528, Car14 BC028528 Aph1a chr3 96963138 96963961 INT_STITCHED_1632 713 Acp6 . Acp6 chr3 100914800 100915619 INT_STITCHED_1639 2609 Ptgfrn . Ptgfrn chr3 100957135 100967876 INT_STITCHED_1640 260 . Ptgfrn Ptgfrn chr3 101993816 102007402 INT_STITCHED_1651 608 Vangl1 Casq2 Vangl1 chr3 102930941 102931790 INT_STITCHED_1656 1207 Dennd2c Bcas2 Dennd2c chr3 102949003 102950801 INT_STITCHED_1657 267 . Dennd2c Dennd2c chr3 104618028 104623683 INT_STITCHED_1662 584 Mov10 . Mov10 chr3 106351238 106351736 INT_STITCHED_1664 4051 Cept1, Dram2 . Cept1 chr3 108391181 108391923 INT_STITCHED_1672 4003 Wdr47 . Wdr47 chr3 116358806 116359743 INT_STITCHED_1685 7347 Hiat1 . Hiatl chr3 116563049 116563725 INT_STITCHED_1687 2868 Frrs1 . Frrs1 chr3 121121824 121122736 INT_STITCHED_1701 355 . Cnn3 Cnn3 chr3 121513631 121513714 INT_STITCHED_1706 8004 Abcd3 . Abcd3 chr3 122136782 122137600 INT_STITCHED_1711 971 . Bcar3 Bcar3 chr3 127155894 127167528 INT_STITCHED_1724 453 . 4930422G04Rik, Larp7 Larp7, Mir302c, Mir302a, Mir302b, Mir302d, Mir367 chr3 129767261 129768048 INT_STITCHED_1735 6486 Sec24b . Sec24b chr3 130973460 130973878 INT_STITCHED_1739 7393 Hadh . Hadh chr3 135099287 135099829 INT_STITCHED_1747 8660 4930539J05Rik, . 4930539J05Rik Ube2d3 chr3 137284970 137285636 INT_STITCHED_1754 3413 Ddit4l . Ddit4l chr3 142423276 142423843 INT_STITCHED_1775 6964 Gtf2b . Gtf2b chr3 157584207 157595548 INT_STITCHED_1814 885 Cth . Cth chr3 157694803 157695284 INT_STITCHED_1815 3887 Srsfl1, Lrrc40 . Srsfl1 chr4 5575140 5577164 INT_STITCHED_1821 1933 Fam110b . Fam110b chr4 6380266 6383720 INT_STITCHED_1823 6789 Nsmaf . Nsmaf chr4 8614996 8616011 INT_STITCHED_1833 2101 Chd7 . Chd7 chr4 10940912 10941926 INT_STITCHED_1839 1366 Plekhf2 . Plekhf2 chr4 11005337 11005975 INT_STITCHED_1841 4993 2310030N02Rik . 2310030N02Rik chr4 13677114 13679150 INT_STITCHED_1855 1395 Runxlt1 Runxlt1 Runxlt1 chr4 13700476 13708564 INT_STITCHED_1856 1357 . Runxlt1 Runxlt1 chr4 i9630174 19631009 INT_STITCHED_1868 3658 Wwp1 . Wwp1 chr4 20704454 20704779 INT_STITCHED_1870 8650 Nkain3 . Nkain3 chr4 21650023 21650732 INT_STITCHED_1871 2045 Ccnc . Ccnc chr4 25722977 25726500 INT_STITCHED_1881 1530 Fut9 . Fut9 chr4 32046934 32047476 INT_STITCHED_1891 8647 Map3k7 . Map3k7 chr4 33035412 33043970 INT_STITCHED_1897 2592 Ankrd6 Ankrd6 Ankrd6 chr4 33071439 33072448 INT_STITCHED_1898 5608 Rragd . Rragd chr4 34501938 34506322 INT_STITCHED_1903 1658 Akirin2 . Akirin2 chr4 34832744 34833418 INT_STITCHED_1905 7860 Zfp292 . Zfp292 chr4 40180008 40186010 INT_STITCHED_1913 1659 Ddx58 . Ddx58 chr4 40803541 40803952 INT_STITCHED_1915 4554 B4galt1 . B4galt1 chr4 41047848 41048517 INT_STITCHED_1917 1551 Aqp3 . Aqp3 chr4 43661458 43661812 INT_STITCHED_1923 6119 Spag8 . Spag8 chr4 45121483 45121498 INT_STITCHED_1932 8010 Tomm5 . Tomm5 chr4 45215967 45216757 INT_STITCHED_1933 3974 . Frmpd1 Frmpd1 chr4 45420433 45421075 INT_STITCHED_1935 3596 Mcart1 . Mcartl chr4 48592304 48592977 INT_STITCHED_1947 4785 Tmeff1 . Tmeff1 chr4 53646937 53647675 INT_STITCHED_1962 7225 Fsd1l . Fsd1l chr4 57932572 57933991 INT_STITCHED_1986 814 D630039A03Rik . D630039A03Rik chr4 59198444 59199036 INT_STITCHED_1991 4924 Ugcg . Ugcg chr4 59593068 59593702 INT_STITCHED_1994 4509 Hsdl2 . Hsdl2 chr4 73903676 73905912 INT_STITCHED_2018 1260 Kdm4c . Kdm4c chr4 80520013 80520803 INT_STITCHED_2024 3576 . D4Bwg0951e D4Bwg0951e chr4 80557651 80558330 INT_STITCHED_2025 1850 D4Bwg0951e . D4Bwg0951e chr4 82047159 82047945 INT_STITCHED_2033 1456 . Nfib Nfib chr4 82153147 82158518 INT_STITCHED_2036 558 Nfib Nfib Nfib chr4 82180557 82189832 INT_STITCHED_2037 7204 . Nfib Nfib chr4 82973975 82976812 INT_STITCHED_2041 343 Ttc39b . Ttc39b chr4 83059982 83060620 INT_STITCHED_2042 2352 Snapc3 . Snapc3 chr4 83164867 83165620 INT_STITCHED_2044 2906 4930473A06Rik . 4930473A06Rik chr4 84854207 84855065 INT_STITCHED_2051 2922 Sh3gl2 . Sh3gl2 chr4 91065881 91066800 INT_STITCHED_2065 4904 Elavl2 . Elavl2 chr4 98394367 98395329 INT_STITCHED_2073 336 L1td1 . L1td1 chr4 99769780 99770611 INT_STITCHED_2084 6051 Ror1 . Ror1 chr4 100451625 100452191 INT_STITCHED_2085 5943 Cachd1 . Cachd1 chr4 101223833 101224306 INT_STITCHED_2087 6107 Dnajc6 . Dnajc6 chr4 104831497 104842867 INT_STITCHED_2096 535 Ppap2b Ppap2b Ppap2b chr4 104868425 104869271 INT_STITCHED_2097 947 . Ppap2b Ppap2b chr4 104896507 104898349 INT_STITCHED_2098 235 . Ppap2b Ppap2b chr4 107035327 107035897 INT_STITCHED_2106 3847 Tmem48 . Tmem48 chr4 107550428 107550830 INT_STITCHED_2107 8621 Magoh . Magoh chr4 107974909 107975592 INT_STITCHED_2112 7080 Zyg11b . Zyg11b chr4 108515672 108516321 INT_STITCHED_2117 5600 Kti12 . Kti12 chr4 110069602 110070245 INT_STITCHED_2124 5744 Agbl4 . Agbl4 chr4 115743638 115744295 INT_STITCHED_2133 4916 Uqcrh, Lrrc41 . Uqcrh chr4 116397804 116398474 INT_STITCHED_2134 5503 Tesk2 . Tesk2 chr4 116825141 116825878 INT_STITCHED_2138 599 Snord38a, . Snord38a Rps8, Snord55 chr4 116924570 116925269 INT_STITCHED_2140 7045 Gm1661, . Gm1661 Tmem53 chr4 117085700 117088622 INT_STITCHED_2143 815 . Rnf220 Rnf220 chr4 118212353 118213114 INT_STITCHED_2147 6341 Tmem125 . Tmem125 chr4 118359572 118360154 INT_STITCHED_2148 2902 Olfr1342 . Olfr1342 chr4 118910530 118911287 INT_STITCHED_2154 4305 Lepre1, . Lepre1 AU022252 chr4 118964429 118965089 INT_STITCHED_2155 7516 Ybx1 . Ybx1 chr4 119076007 119084885 INT_STITCHED_2156 4562 Ccdc30 . Ccdc30 chr4 119170858 119171363 INT_STITCHED_2157 4607 Rimkla . Rimkla chr4 119487998 119488754 INT_STITCHED_2160 1604 Hivep3 . Hivep3 chr4 119831385 119832062 INT_STITCHED_2161 3892 Edn2 . Edn2 chr4 122514588 122515039 INT_STITCHED_2172 5193 Ppt1 . Ppt1 chr4 122676422 122676991 INT_STITCHED_2173 7715 Mycl1 . Mycl1 chr4 124811451 124811907 INT_STITCHED_2185 641 Zc3h12a . Zc3h12a chr4 125779943 125780736 INT_STITCHED_2196 2275 Lsm10, Stk40 . Stk40 chr4 126142985 126143622 INT_STITCHED_2198 1019 Eif2c1 . Eif2c1 chr4 126741328 126741791 INT_STITCHED_2202 4312 Zmym1 . Zmym1 chr4 126801236 126802125 INT_STITCHED_2203 2032 Gm12942 . Gm12942 chr4 127021763 127022891 INT_STITCHED_2208 690 . Gjb3, Gjb5 Gjb5 chr4 128334780 128335398 INT_STITCHED_2211 5180 Phc2 . Phc2 chr4 128405346 128406067 INT_STITCHED_2212 8615 Phc2 . Phc2 chr4 128556315 128556889 INT_STITCHED_2213 2454 Trim62 . Trim62 chr4 129050358 129052712 INT_STITCHED_2218 255 Zbtb8a . Zbtb8a chr4 129221212 129221953 INT_STITCHED_2219 5426 Hdac1 . Hdac1 chr4 129779132 129780024 INT_STITCHED_2222 1812 Pef1 Tinagl1 Pef1 chr4 130213352 130214031 INT_STITCHED_2225 2627 Pum1 . Pum1 chr4 132061470 132062305 INT_STITCHED_2233 2028 Sesn2 . Sesn2 chr4 133371377 133372545 INT_STITCHED_2245 436 . Arid1a, Pigv Arid1a, chr4 133567462 133568053 INT_STITCHED_2248 2013 . Lin28a Lin28a chr4 134406960 134407757 INT_STITCHED_2251 7098 Tmem57 . Tmem57 chr4 135137211 135138212 INT_STITCHED_2256 1300 . Grhl3 Grhl3 chr4 135702424 135703370 INT_STITCHED_2258 1210 Id3 . Id3 ch14 135847102 135847490 INT_STITCHED_2260 5446 Zfp46 . Zf4J46 chr4 135873252 135874283 INT_STITCHED_2261 3874 Hnrnpr . Hnrnpr chr4 136016956 136019978 INT_STITCHED_2262 655 Luzp1 . Luzp1 chr4 137025750 137026764 INT_STITCHED_2264 587 Hspg2 . Hspg2 chr4 137879059 137879857 INT_STITCHED_2271 4511 Pink1 . Pink1 chr4 139520165 139520892 INT_STITCHED_2282 3096 Klhdc7a . Klhdc7a chr4 140200327 140201030 INT_STITCHED_2286 3387 Arhgef101 . Arhgef101 chr4 140249934 140251467 INT_STITCHED_2287 1738 Rcc2 . Rcc2 chr4 140515660 140516266 INT_STITCHED_2288 3301 Sdhb . Sdhb chr4 141154043 141155058 INT_STITCHED_2293 509 Fblim1 . Fblim1 chr4 141784495 141791290 INT_STITCHED_2298 1170 9030409G11Rik . 9030409G11Rik chr4 142891686 142896659 INT_STITCHED_2306 555 Pdpn . Pdpn chr4 147407829 147408586 INT_STITCHED_2316 2518 Clcn6, Mthfr . Clcn6 chr4 149604905 149605684 INT_STITCHED_2326 1574 Eno1, Gm5506 . Eno1 chr4 150415590 150416311 INT_STITCHED_2333 7184 Per3 . Per3 chr4 151373388 151381390 INT_STITCHED_2335 1548 Klhl21,Phf13 . Klhl21 chr4 151417116 151417695 INT_STITCHED_2336 4939 Nol9, Tas1r1 . Nol9 chr4 151559144 151559677 INT_STITCHED_2337 3681 Acot7 Acot7 Acot7 chr4 151664406 151665150 INT_STITCHED_2338 3943 Icmt . Icmt chr4 153469755 153470645 INT_STITCHED_2346 2164 Trp73 . Trp73 chr4 155043894 155044798 INT_STITCHED_2356 991 Mib2 . Mib2 chr4 155562905 155563924 INT_STITCHED_2358 1143 Agrn . Agrn chr5 5698769 5699506 INT_STITCHED_2369 3137 Steap2 . Steap2 chr5 8423915 8424874 INT_STITCHED_2372 1629 Slc25a40, . Slc25a40 Dbf4 chr5 20389584 20390410 INT_STITCHED_2405 3630 Phtf2, Tmem60 . Phtf2 chr5 21144388 21144924 INT_STITCHED_2410 7716 Fbxl13 . Fbxl13 chr5 21157440 21158426 INT_STITCHED_2411 5853 Fbxl13, Armc10 . Armc10 chr5 21237845 21238483 INT_STITCHED_2412 7016 Pmpcb . Pmpcb chr5 24190157 24190688 INT_STITCHED_2425 4368 Nub1 . Nub1 chr5 24515415 24516073 INT_STITCHED_2426 2110 . Prkag2 Prkag2 chr5 25038744 25042771 INT_STITCHED_2428 863 1700096K18Rik Mll3, 1700096K18Rik 4831440E17Rik chr5 25266891 25267570 INT_STITCHED_2431 3382 Actr3b . Actr3b chr5 27368835 27369369 INT_STITCHED_2438 8605 Dpp6 . Dpp6 chr5 29525401 29526304 INT_STITCHED_2446 2338 Rnf32 . Rnf32 chr5 30063886 30064743 INT_STITCHED_2450 3241 Dnajb6, . Dnajb6 Gm5129 chr5 31791484 31795140 INT_STITCHED_2453 1536 4930548H24Rik, . Gpn1 Gpn1 chr5 32918629 32919653 INT_STITCHED_2458 8602 Yes1 . Yes1 chr5 33444956 33450141 INT_STITCHED_2461 2733 Slc5a1 . Slc5a1 chr5 35447171 35447793 INT_STITCHED_2473 2708 Lrpap1 . Lrpap1 chr5 37188271 37189788 INT_STITCHED_2477 1412 Mrfap1 . Mrfap1 chr5 44251617 44261048 INT_STITCHED_2494 503 Cd38 . Cd38 chr5 45886696 45887517 INT_STITCHED_2497 2501 Lap3 . Lap3 chr5 45906343 45906785 INT_STITCHED_2498 5778 Med28 . Med28 chr5 53857769 53859125 INT_STITCHED_2508 1228 . Rbpj Rbpj chr5 53983387 53983835 INT_STITCHED_2512 4655 Rbpj . Rbpj chr5 64362131 64362846 INT_STITCHED_2524 8593 Rell1 . Rell1 chr5 64486701 64494650 INT_STITCHED_2526 3034 Pgm1 . Pgm1 chr5 64891420 64892157 INT_STITCHED_2531 506 . Klf3 Klf3 chr5 64970809 64971754 INT_STITCHED_2532 2035 . Klf3 Klf3 chr5 65038454 65039558 INT_STITCHED_2533 747 . Klf3 Klf3 chr5 65203049 65203823 INT_STITCHED_2534 605 . Klf3 Klf3 chr5 65521902 65522600 INT_STITCHED_2537 3759 Klhl5 . Klhl5 chr5 65832295 65833237 INT_STITCHED_2539 4448 Ugdh . Ugdh chr5 66091258 66091720 INT_STITCHED_2541 5666 Pds5a . Pds5a chr5 66153811 66154536 INT_STITCHED_2543 8591 N4bp2 . N4bp2 chr5 66542614 66545335 INT_STITCHED_2544 1354 Rbm47 . Rbm47 chr5 68240570 68241089 INT_STITCHED_2556 4241 Atp8a1 . Atp8a1 chr5 75972506 75973498 INT_STITCHED_2583 2620 Kit . Kit chr5 76798260 76799006 INT_STITCHED_2588 2195 Nmu . Nmu chr5 77339613 77340383 INT_STITCHED_2590 8032 Aasdh . Aasdh ch15 77683194 77694467 INT_STITCHED_2593 238 Rest . Rest chr5 89108097 89114909 INT_STITCHED_2614 1675 Grsf1 . Grsf1 chr5 92926941 92933665 INT_STITCHED_2621 904 Scarb2 . Scarb2 chr5 93112043 93112714 INT_STITCHED_2624 5586 Shroom3 . Shroom3 chr5 93322548 93323285 INT_STITCHED_2626 3484 Shroom3 . Shroom3 chr5 100472593 100473735 INT_STITCHED_2652 2432 Enoph1, . Enoph1 Hnrpdl chr5 101101211 101101831 INT_STITCHED_2655 2682 Coq2 . Coq2 chr5 103847896 103848433 INT_STITCHED_2669 5025 Ptpn13 . Ptpn13 chr5 104862866 104872330 INT_STITCHED_2676 320 Spp1 . Spp1 chr5 109097366 109098181 INT_STITCHED_2691 2714 Idua, Slc26a1 . Idua chr5 110527885 110528617 INT_STITCHED_2695 2800 Plcxd1 . Plcxd1 chr5 110656201 110658296 INT_STITCHED_2696 2455 Ankle2 . Ankle2 chr5 110897904 110899242 INT_STITCHED_2700 292 . Fbrsl1 Fbrsl1 chr5 111232926 111236161 INT_STITCHED_2702 276 Ulk1 Ulk1 Ulk1 chr5 111306460 111307534 INT_STITCHED_2703 4183 Ttc28 . Ttc28 chr5 113915656 113916217 INT_STITCHED_2715 5417 Wscd2 . Wscd2 chr5 114725389 114725938 INT_STITCHED_2720 3071 Foxn4 . Foxn4 chr5 115021009 115022171 INT_STITCHED_2724 1268 BC057022 . BC057022 chr5 115721625 115722390 INT_STITCHED_2727 1373 Rnf10 . Rnf10 chr5 115750818 115751483 INT_STITCHED_2728 1977 Dynll1 . Dynll1 chr5 115886385 115894671 INT_STITCHED_2732 368 . Msi1 Msi1 chr5 115929383 115929949 INT_STITCHED_2733 390 Sirt4 . Sirt4 chr5 116739839 116740353 INT_STITCHED_2735 4769 Ccdc60 . Ccdc60 chr5 117764474 117765420 INT_STITCHED_2741 2391 Vsig10 Wsb2 Vsig10 chr5 121986673 121990552 INT_STITCHED_2757 2098 Mapkapk5 . Mapkapk5 chr5 123607764 123608595 INT_STITCHED_2771 1902 . Rhof Rhof chr5 123840532 123840817 INT_STITCHED_2773 7999 Mlxip . Mlxip chr5 128103516 128103953 INT_STITCHED_2789 8575 Slc15a4 . Slc15a4 chr5 129105766 129110009 INT_STITCHED_2794 828 5930412G12Rik, . 5930412G12Rik Fzd10 chr5 129459327 129459946 INT_STITCHED_2795 4878 Rimbp2 . Rimbp2 chr5 130216498 130217009 INT_STITCHED_2801 4380 Mrps17 . Mrps17 chr5 130234026 130234832 INT_STITCHED_2802 4152 Gbas . Gbas chr5 130363609 130364562 INT_STITCHED_2803 8574 Chchd2 . Chchd2 chr5 134654188 134654880 INT_STITCHED_2825 1841 Wbscr16, . Wbscr16 Gtf2ird2 chr5 135402290 135403027 INT_STITCHED_2829 1370 Wbscr27 . Wbscr27 chr5 135476827 135477544 INT_STITCHED_2832 1445 Wbscr25 Abhd11 Wbscr25 chr5 136105127 136105914 INT_STITCHED_2834 3937 Rhbdd2 . Rhbdd2 chr5 136410740 136412181 INT_STITCHED_2838 736 Ywhag . Ywhag chr5 137747012 137747785 INT_STITCHED_2845 2219 Srrt . Srrt chr5 137778171 137778873 INT_STITCHED_2846 2182 Slc12a9 . Slc12a9 chr5 137792787 137793553 INT_STITCHED_2847 3627 Ephb4 . Ephb4 chr5 138531655 138532586 INT_STITCHED_2849 4057 Zkscan1 . Zkscan1 chr5 139675717 139676582 INT_STITCHED_2854 1584 Sun1 . Sun1 chr5 139734064 139734931 INT_STITCHED_2855 4824 Get4 . Get4 chr5 141087076 141088486 INT_STITCHED_2864 1220 Lfng . Lfrig chr5 143022054 143037530 INT_STITCHED_2874 494 Radi1 . Radi1 chr5 143543892 143544993 INT_STITCHED_2876 2397 . Tnrc18 Tnrc18 chr5 143560794 143579912 INT_STITCHED_2877 946 Tnrc18 Tnrc18 Tnrc18 chr5 141718476 143719226 INT_STITCHED_2878 3909 Fscn1 . Fscn1 chr5 149350152 149362682 INT_STITCHED_2907 864 Ubl3 . Ubl3 chr5 149556262 149556865 INT_STITCHED_2910 3402 2210417A02Rik . 2210417A02Rik chr6 7644080 7663321 INT_STITCHED_2939 847 Asns . Asns chr6 15664027 15664459 INT_STITCHED_2958 5388 Mdfic . Mdfic chr6 30109355 30110097 INT_STITCHED_2995 772 Mir182 Mir183, Mir182 Mir96 chr6 37384202 37386490 INT_STITCHED_3028 3134 Creb3l2 . Creb3l2 chr6 38242963 38243836 INT_STITCHED_3037 5549 Zc3hav1l . Zc3hav1l chr6 42205849 42206459 INT_STITCHED_3058 7001 Tmem139 . Tmem139 chr6 50066065 50074818 INT_STITCHED_3072 1637 Mpp6 . Mpp6 chr6 50209997 50210610 INT_STITCHED_3073 6221 Dfna5 . Dfna5 chr6 51483276 51494780 INT_STITCHED_3078 826 Snx10 . Snx10 chr6 51956055 51963851 INT_STITCHED_3081 577 Skap2 . Skap2 chr6 52103875 52104482 INT_STITCHED_3084 5045 Hoxa1 . Hoxa1 chr6 54914440 54915345 INT_STITCHED_3101 1628 Nod1 . Nod1 chr6 66980137 66981045 INT_STITCHED_3129 2263 Gadd45a Gadd45a Gadd45a chr6 71575730 71576551 INT_STITCHED_3144 3531 Kdm3a . Kdm3a chr6 72502671 72503229 INT_STITCHED_3147 2910 Capg . Capg chr6 72703827 72708966 INT_STITCHED_3150 1561 . Tcf7l1 Tcf7l1 chr6 72736980 72745613 INT_STITCHED_3151 634 Tcf7l1 Tcf7l1 Tcf7l1 chr6 72848028 72848774 INT_STITCHED_3153 5856 Kcmf1 . Kcmf1 chr6 82710614 82711291 INT_STITCHED_3177 2460 . Hk2 Hk2 chr6 84012527 84015422 INT_STITCHED_3186 1066 . Zfml, Dysf Dysf chr6 85024817 85025619 INT_STITCHED_3191 5735 Exoc6b . Exoc6b chr6 87863162 87864161 INT_STITCHED_3199 1880 8430410A17Rik . 8430410A17Rik chr6 92196225 92198121 INT_STITCHED_3219 1001 Trh . Trh chr6 97051422 97052960 INT_STITCHED_3248 492 . Fam19a4 Fam19a4 chr6 98979333 98980035 INT_STITCHED_3262 2081 Foxp1 . Foxp1 chr6 100235278 10023657 INT_STITCHED_3276 4629 Rybp . Rybp chr6 100369906 100372686 INT_STITCHED_3279 988 . Rybp Rybp chr6 108020709 108021593 INT_STITCHED_3290 2984 Setmar . Setmar chr6 112899075 112900921 INT_STITCHED_3305 1751 Srgap3 . Srgap3 chr6 113452636 113453205 INT_STITCHED_3310 4977 Prrt3 . Prrt3 chr6 113566995 113567675 INT_STITCFIED_3311 7573 Vhl . Vhl chr6 115633121 115635841 INT_STITCHED_3320 1845 Raf1 . Raf1 chr6 116148172 116148826 INT_STITCHED_3324 4749 Tmcc1 . Tmcc1 chr6 119274532 119275309 INT_STITCHED_3331 2012 Lrtm2 . Lrtm2 chr6 119364465 119369724 INT_STITCHED_3332 869 Adipor2 . Adipor2 chr6 120241456 120242188 INT_STITCHED_3335 2421 B4galnt3 . B4galnt3 chr6 122316022 122317010 INT_STITCHED_3343 278 . Phc1 Phc1 chr6 122558176 122559103 INT_STITCHED_3345 907 Gdf3, Apobec1 . Gdf3 chr6 122574257 122575075 INT_STITCHED_3346 1790 Dppa3 . Dppa3 chr6 124754367 124755031 INT_STITCHED_3353 6468 Spsb2 . Spsb2 chr6 124781521 124782304 INT_STITCHED_3354 3019 Cdca3, Usp5 . Cdca3 chr6 125146126 125147005 INT_STITCHED_3357 2986 Mrpl51, Ncapd2 . Mrpl51 chr6 127053459 127054097 INT_STITCHED_3369 3276 9630033F20Rik . 9630033F20Rik chr6 128092062 128092947 INT_STITCHED_3375 2085 Tspan9 . Tspan9 chr6 128395390 128396444 INT_STITCHED_3380 1491 . Gm10069, Gm10069 Fkbp4 chr6 134839572 134840045 INT_STITCHED_3399 7135 Gpr19 . Gpr19 chr6 135016609 135017490 INT_STITCHED_3402 2909 Gprc5a . Gprc5a chr6 135143600 135144185 INT_STITCHED_3403 7525 8430419L09Rik . 8430419L09Rik chr6 137118500 137119078 INT_STITCHED_3414 4375 Rerg . Rerg chr6 142910352 142911545 INT_STITCHED_3433 1851 St8sia1 . St8sia1 chr6 142969103 142969851 INT_STITCHED_3435 1647 . St8sia1, St8sia1 5730419I09Rik chr6 143119001 143119729 INT_STITCHED_3439 5592 Etnk1 . Etnk1 chr6 144997218 145010452 INT_STITCHED_3446 738 Bcat1 . Bcat1 chr6 146668166 146674748 INT_STITCHED_3453 2469 Stk381 . Stk381 chr6 148894789 148906259 INT_STITCHED_3463 362 Fam60a . Fam60a chr6 149260435 149261383 INT_STITCHED_3466 2613 2810474O19Rik . 2810474O19Rik chr7 4076531 4077316 INT_STITCHED_3470 1222 9430041J12Rik, Leng9 9430041J12Rik Ttyh1 chr7 4487732 4488465 INT_STITCHED_3473 7092 6030429G01Rik . 6030429G01Rik chr7 4703001 4704500 INT_STITCHED_3474 696 Cox6b2 . Cox6b2 chr7 7085385 7086148 INT_STITCHED_3480 2995 Zfp773 . Zfp773 chr7 20045717 20046525 INT_STITCHED_3486 3637 Mark4 . Mark4 chr7 20093826 20094324 INT_STITCHED_3487 7263 Bloc1s3, . Bloc1s3 Trappc6a chr7 20157934 20161677 INT_STITCHED_3488 357 Gemin7 Gemin7, Gemin7 Zfp296 chr7 20326833 20328288 INT_STITCHED_3489 579 . Pvrl2 Pvrl2 chr7 20400342 20402067 INT_STITCHED_3490 649 Bcl3 Bcl3 Bcl3 chr7 74877697 94873996 INT_STITCHFD_3492 4012 Zfp180 . Zfp180 chr7 25289770 25302672 INT_STITCHED_3493 236 Zfp428 Zfp428 Zfp428 chr7 25664201 25665192 INT_STITCHED_3495 3298 Rps19 . Rps19 chr7 25998956 25999482 INT_STITCHED_3498 4323 Dedd2 . Dedd2 chr7 26048760 26049461 INT_STITCHED_3499 530 . Erf Erf chr7 27965321 27966083 INT_STITCHED_3504 2673 Rab4b, Mia1 . Rab4b chr7 27983767 27984476 INT_STITCHED_3505 3541 Snrpa . Snrpa chr7 28043302 28043716 INT_STITCHED_3506 2757 Numbl . Numbl chr7 28518631 28521086 INT_STITCHED_3510 1758 Zfp60 . Zfp60 chr7 28624916 28625830 INT_STITCHED_3511 1744 Zfp59 . Zfp59 chr7 29363488 29364974 INT_STITCHED_3513 845 . Pak4 Pak4 chr7 29420248 29420834 INT_STITCHED_3514 4991 C330005M16Rik . C330005M16Rik chr7 29477392 29478200 INT_STITCHED_3515 1927 Fbxo27 . Fbxo27 chr7 30078547 30079377 INT_STITCHED_3517 1761 Ppp1r14a Ppp1r14a Ppp1r14a chr7 30757305 30768472 INT_STITCHED_3520 612 Zfp568 Zfp74 Zfp568 chr7 30872494 30873179 INT_STITCHED_3522 7178 Zfp566 . Zfp566 chr7 31372373 31372940 INT_STITCHED_3526 4996 Zbtb32, . Wbp7 Wbp7 chr7 31392634 31393353 INT_STITCHED_3527 1582 Upkla Wbp7, Upkla Prodh2 chr7 31937273 31938066 INT_STITCHED_3530 4926 Gramd1a . Gramd1a chr7 34949720 34950749 INT_STITCHED_3531 8526 Uba2 . Uba2 chr7 35437649 35438290 INT_STITCHED_3532 2994 Kctd15 . Kctd15 chr7 36107701 36120798 INT_STITCHED_3535 610 Gpatch1, . Rhpn2 Rhpn2 chr7 38338600 38339282 INT_STITCHED_3547 2440 . Zfp536 Zfp536 chr7 50862978 50863932 INT_STITCHED_3560 1804 Zfp819 . Zfp819 chr7 51630296 51631278 INT_STITCHED_3562 1315 1700008O03Rik Syt3 1700008O03Rik chr7 51954357 51964325 INT_STITCHED_3565 582 Izumo2 . Izumo2 chr7 52878661 52879259 INT_STITCHED_3569 6738 Izumo1, . Izumo1 Rasip1, Fut1 chr7 54053865 54054483 INT_STITCHED_3571 5445 Gtf2h1, . Gtf2h1 Hps5 chr7 57029746 57030493 INT_STITCHED_3581 4420 Prmt3 . Prmt3 chr7 70585007 70585674 INT_STITCHED_3600 7567 Otud7a . Otud7a chr7 72302006 72302711 INT_STITCHED_3608 4605 Fam189a1 . Fam189a1 chr7 75418913 75421020 INT_STITCHED_3619 2227 Fam169b . Fam169b chr7 80286018 80286585 INT_STITCHED_3632 4127 . Rgma Rgma chr7 80531416 80545623 INT_STITCHED_3636 1261 . Rgma Rgma chr7 80679726 80684471 INT_STITCHED_3637 512 Chd2 Chd2 chr7 86284126 86284802 INT_STITCHED_3651 4132 . Hapin3 Hapin3 chr7 86423381 86424010 INT_STITCHED_3653 4382 Abhd2 . Abhd2 chr7 86799396 86806853 INT_STITCHED_3657 741 5730590G19Rik . 5730590G19Rik chr7 87253990 87254677 INT_STITCHED_3660 8111 Idh2 . Idh2 chr7 87954066 87954752 INT_STITCHED_3666 4847 Iqgap1 . Iqgap1 chr7 88208035 88208759 INT_STITCHED_3671 2017 A1pk3 . A1pk3 chr7 95578089 95578712 INT_STITCHED_3691 5604 Rab38 . Rab38 chr7 96490332 96490891 INT_STITCHED_3692 4627 Tmem135 . Tmem135 chr7 97123764 97124610 INT_STITCHED_3695 2094 Eed . Eed chr7 97410448 97410819 INT_STITCHED_3698 6727 Ccdc83 . Ccdc83 chr7 103353190 103354078 INT_STITCHED_3713 1669 Odz4 . Odz4 chr7 107377250 107377769 INT_STITCHED_3734 7819 Pgm2l1 . Pgm2l1 chr7 107436366 107436962 INT_STITCHED_3735 7651 P4ha3 . P4ha3 chr7 107848144 107849130 INT_STITCHED_3738 1234 Fam168a . Fam168a chr7 109248288 109249058 INT_STITCHED_3741 1466 Artl1,Art5 . Art1 chr7 111392319 111392670 INT_STITCHED_3744 5692 Trim34 . Trim34 chr7 112551030 112551509 INT_STITCHED_3746 7631 Fam160a2 . Fam160a2 chr7 114351139 114351754 INT_STITCHED_3748 3262 Rbmxl2 . Rbmxl2 chr7 121782144 121782733 INT_STITCHED_3780 2434 Calca . Calca chr7 121883989 121884609 INT_STITCHED_3781 2465 Tnsc . Insc chr7 125723349 125724114 INT_STITCHED_3793 5085 Tmc7 . Tmc7 chr7 127040059 127042484 INT_STITCHED_3801 448 Dcun1d3, . Dcun1d3 Lyrm1 chr7 130354891 130355503 INT_STITCHED_3820 2662 Slc5a11 . Slc5a11 chr7 133520840 133521647 INT_STITCHED_3830 1910 Spns1 . Spns1 chr7 133535744 133536602 INT_STITCHED_3831 4899 Nfatc2ip . Nfatc2ip chr7 134367327 134369311 INT_STITCHED_3833 282 Sept1 Mylpf, 1-Sep Sept1 chr7 134659607 134660269 INT_STITCHED_3834 5484 1700008J07Rik . 1700008J07Rik chr7 134912208 134912952 INT_STITCHED_3835 1928 Orai3 . Orai3 chr7 137395511 137408698 INT_STITCHED_3841 529 Fgfr2 Fgfr2 Fgfr2 chr7 138004134 138005002 INT_STITCHED_3845 2881 Plekha1 . Plekha1 chr7 139807718 139808551 INT_STITCHED_3853 1520 Lhpp . Lhpp chr7 140000477 140001636 INT_STITCHED_3854 2558 Fam53b . Fam53b chr7 146041339 146048877 INT_STITCHED_3884 388 Ppp2r2d, . Ppp2r2d Mapk1ip1 chr7 148026799 148027562 INT_STITCHED_3894 2582 1190003J15Rik . 1190003J15Rik chr7 148124539 148125460 INT_STITCHED_3895 6228 Athl1 BC024386 Athl1 chr7 148144326 148149350 INT_STITCHED_3896 269 Ifitm1, BC024386, Ifitm2 Ifitm2 Ifitm3 chr7 148210613 148212675 INT_STITCHED_3898 1559 . Ifitm3 Ifitm3 chr7 149767035 149767709 INT_STITCHED_3903 8496 H19 . H19 chr8 3394398 3401126 INT_STITCHED_3919 466 Arhgef18 . Arhgef18 chr8 4341931 4370480 INT_STITCHED_3923 630 Ccl25 . Ccl25 chr8 8655610 8656423 INT_STITCHED_3932 8493 Efnb2 . Efnb2 chr8 10924754 10925468 INT_STITCHED_3939 2611 3930402G23Rik . 3930402G23Rik chr8 11640471 11650624 INT_STITCHED_3941 1100 Ankrd10 Ankrd10 Ankrd10 chr8 12481728 12482441 INT_STITCHED_3946 1518 . Sox1 Sox1 chr8 12759924 12760464 INT_STITCHED_3951 3049 Atp11a . Atp11a chr8 12928814 12929349 INT_STITCHED_3953 2295 . Mcf2l Mcf2l chr8 23526226 23527098 INT_STITCHED_3973 2380 Mrps31 . Mrps31 chr8 23913976 23914613 INT_STITCHED_3975 4178 Ap3m2 . Ap3m2 chr8 24360828 24361492 INT_STITCHED_3979 1685 Golga7 . Golga7 chr8 24470989 24471980 INT_STITCHED_3980 3038 . Sfrp1 Sfrp1 chr8 24509604 24521644 INT_STITCHED_3981 472 Sfrp1 Sfrp1 Sfrp1 chr8 25555859 25556317 INT_STITCHED_3986 6273 1810011O10Rik . 1810011O10Rik chr8 26623789 26624247 INT_STITCHED_3990 2962 Fgfr1 . Fgfr1 chr8 26863847 26864429 INT_STITCHED_3992 4336 Ddhd2 . Ddhd2 chr8 32280929 32281569 INT_STITCHED_4004 4366 Mak16 . Mak16 chr8 41720049 41720645 INT_STITCIIED_4039 2047 Mtmr7 . Mtmr7 chr8 42048148 42048839 INT_STITCHED_4041 1897 . Pdgfrl, Pdgfrl Frg1, Mtus1 chr8 42217833 42218697 INT_STITCHED_4043 2284 Mtus1 . Mtus1 chr8 44265400 44266109 INT_STITCHED_4044 408 Triml2 . Triml2 chr8 44392194 44392898 INT_STITCHED_4045 289 Zfp42 . Zfp42 chr8 47299342 47299968 INT_STITCHED_4051 7463 Slc25a4 . Slc25a4 chr8 47704015 47704883 INT_STITCHED_4054 4022 Casp3, . Casp3 Ccde111 chr8 48424007 48424844 INT_STITCHED_4059 1569 . Stox2 Stox2 chr8 55161375 55162311 INT_STITCHED_4071 913 Vegfc . Vegfc chr8 59968722 59969274 INT_STITCHED_4078 2709 Sap30 . Sap30 chr8 67475993 67476480 INT_STITCHED_4094 5721 Tmem192 . Tmem192 chr8 70794823 70795320 INT_STITCHED_4105 4825 Sh2d4a . Sh2d4a chr8 72797791 72798792 INT_STITCHED_4113 1697 . Homer3 Homer3 chr8 75076675 75085391 INT_STITCHED_4119 501 Med26 Med26 Med26 chr8 82579447 82580481 INT_STITCHED_4146 4901 Hhip . Hhip chr8 85678936 85684999 INT_STITCHED_4154 1067 Tbc1d9 Tbc1d9 Tbc1d9 chr8 86114380 86114994 INT_STITCHED_4156 4890 Tecr . Tecr chr8 86701216 86703034 INT_STITCHED_4158 1364 Mir181d, . Mir181d Mir181c chr8 86718129 86718656 INT_STITCHED_4159 832 . Nanos3, Mir23a Mir181d, Mir181c, Mir24-2, Mir27a, Mir23a chr8 87438974 87439767 INT_STITCHED_4165 915 Dnase2a . Dnase2a chr8 88022293 88023151 INT_STITCHED_4168 2230 Gpt2 . Gpt2 chr8 89411697 89412634 INT_STITCHED_4172 1024 N4bp1 . N4bp1 chr8 91569015 91569562 INT_STITCHED_4180 1801 Sall1 . Sall1 chr8 91795502 91796285 INT_STITCHED_4183 1473 . Sall1 Sall1 chr8 93375315 93376069 INT_STITCHED_4191 2318 . Chd9 Chd9 chr8 93405177 93406102 INT_STITCHED_4192 2533 . Chd9 Chd9 chr8 93427969 93428698 INT_STITCHED_4193 1106 . Chd9 Chd9 chr8 96557414 96558124 INT_STITCHED_4213 5469 Ogfod1, . Nudt21 Nudt21 chr8 97446210 97446860 INT_STITCHED_4216 1878 Ccdc102a . Ccdc102a chr8 97667312 97668037 INT_STITCHED_4217 1672 Kifc3 . Kifc3 chr8 98052059 98056627 INT_STITCHED_4218 956 Ccdc113 . Ccdc113 chr8 98220746 98221252 INT_STITCHED_4219 6116 Ndrg4 . Ndrg4 chr8 107751860 107757896 INT_STITCHED_4233 914 D230025D16Rik D230025D16Rik D230025D16Rik chr8 108495132 108495876 INT_STITCHED_4235 3388 Slc12a4 Slc12a4 Slc12a4 chr8 109811081 109811921 INT_STITCHED_4244 2689 Nfat5 . Nfat5 chr8 110118419 110119429 INT_STITCHED_4245 1265 Psmd7 . Psmd7 chr8 111246518 111254244 INT_STITCHED_4251 508 . Zfhx3 Zfhx3 chr8 112216041 112217027 INT_STITCHED_4256 1943 2400003C14Rik . 2400003C14Rik chr8 112397963 112409627 INT_STITCHED_4257 3668 Phlpp2 . Phlpp2 chr8 114064905 114065322 INT_STITCHED_4260 4168 Znrf1 . Znrf1 chr8 114136803 114146846 INT_STITCHED_4262 2102 . Znrf1, Ldhd Ldhd chr8 114172500 114175132 INT_STITCHED_4263 823 Zfp1 Ldhd Zfp1 chr8 119498759 119499379 INT_STITCHED_4282 2905 1700030J22Rik . 1700030J22Rik chr8 119683409 119683904 INT_STITCHED_4284 6290 Gan . Gan chr8 120017171 120028015 INT_STITCHED_4287 1135 Plcg2 Plcg2 Plcg2 chr8 120809727 120810433 INT_STITCHED_4290 8471 Cdh13 . Cdh13 chr8 123033008 123033772 INT_STITCHED_4299 1429 . Gse1 Gse1 chr8 123056306 123057280 INT_STITCHED_4300 631 . Gse1 Gse1 chr8 123195397 123196271 INT_STITCHED_4301 3438 Cox4nb, . Cox4i1 Cox4i1 chr8 125857754 125858952 INT_STITCHED_4304 2207 Spire2 . Spire2 chr8 125899749 125900605 INT_STITCHED_4305 8468 Tcf25 Tubb3 Tcf25 chr8 126330309 126331154 INT_STITCHED_4309 2390 Rab4a . Rab4a chr8 126535550 126538752 INT_STITCHED_4311 2203 Taf5l . Taf5l chr8 128189605 128190453 INT_STITCHED_4323 2510 4933403G14Rik . 4933403G14Rik chr9 15081242 15081878 INT_STITCHED_4375 6833 Med17 . Med17 chr9 20257900 20258612 INT_STITCHED_4389 4697 Zfp26 . Zfp26 chr9 20782392 20784089 INT_STITCHED_4391 266 S1pr2 . S1pr2 chr9 21222272 21222788 INT_STITCHED_4392 3282 Qtrt1 . Qtrt1 chr9 21566312 21573527 INT_STITCHED_4395 309 Spc24 Spc24 Spc24 chr9 21652171 21652836 INT_STITCHED_4397 2144 Dock6 . Dock6 chr9 21941572 21942182 INT_STITCHED_4398 1823 Acp5 . Acp5 chr9 26965221 26965892 INT_STITCHED_4409 6637 Jam3 . Jam3 chr9 30840106 30840580 INT_STITCHED_4423 5243 Zbtb44 . Zbtb44 chr9 34919369 34920459 INT_STITCHED_4441 1254 St3gal4, St3gal4, 4930581F22Rik 4930581E22Rik 4930581F22Rik chr9 36601807 36611238 INT_STITCHED_4443 929 Ei24 . Ei24 chr9 37056042 37056855 INT_STITCHED_4448 5381 Slc37a2 . Slc37a2 chr9 37292583 37293531 INT_STITCHED_4449 1633 BC024479 . BC024479 chr9 43537646 43538191 INT_STITCHED_4476 1993 . Pvrl1 Pvrl1 chr9 44119256 4420060 INT_STITCHED_4481 4619 Hinfp . Hinfp chr9 44141293 44142111 INT_STITCHED_4482 302 Dpagt1, . H2afx H2afx chr9 45649159 45649717 INT_STITCHED_4488 8454 Bace1 . Bace1 chr9 47341278 47342102 INT_STITCHED_4500 5543 Cadm1 . Cadm1 chr9 48647618 48648098 INT_STITCHED_4507 6925 Zbtb16 . Zbtb16 chr9 48799482 48800362 INT_STITCHED_4509 1285 Usp28 . Usp28 chr9 48862028 48862859 INT_STITCHED_4511 5295 Zw10 . Zw10 chr9 49559299 49560181 INT_STITCHED_4519 1413 . Ncam1 Ncam1 chr9 49604426 49604976 INT_STITCHED_4520 2399 Ncam1 . Ncam1 chr9 49743610 49744745 INT_STITCHED_4521 1765 . Ncam1 Ncam1 chr9 51854804 51855366 INT_STITCHED_4527 8453 Rdx, Gm6981 . Rdx chr9 53618496 53619776 INT_STITCHED_4531 781 Slc35f2 . Slc35f2 chr9 54703743 54705821 INT_STITCHED_4539 1908 Ireb2 . Ireb2 chr9 55063210 55073663 INT_STITCHED_4542 285 Fbxo22 . Fbxo22 chr9 57010741 57014562 INT_STITCHED_4548 2444 Commd4 . Commd4 chr9 57358103 57371993 INT_STITCHED_4549 395 Cox5a . Cox5a chr9 57677536 57678655 INT_STITCHED_4550 2513 Arid3b . Arid3b chr9 60635345 60636054 INT_STITCHED_4568 2794 Uaca . Uaca chr9 61208965 61209654 INT_STITCHED_4575 1542 . Tle3 Tle3 chr9 61233897 61234814 INT_STITCHED_4576 4412 . Tle3 Tle3 chr9 62185724 62186999 INT_STITCHED_4582 2018 Anp32a . Anp32a chr9 62383015 62383432 INT_STITCHED_4585 7274 Coro2b . Coro2b chr9 64988516 64989016 INT_STITCHED_4595 8450 Igdec3 . Igdcc3 chr9 65186892 65195417 INT_STITCHED_4598 1055 Pdcd7 . Pdcd7 chr9 65441290 65442044 INT_STITCHED_4599 1266 Pif1 . Pif1 chr9 67056190 67062471 INT_STITCHED_4607 611 . Tpm1 Tpm1 chr9 70067253 70071655 INT_STITCHED_4620 3207 . Myo1e Myo1e chr9 72505560 72506130 INT_STITCHED_4635 4790 Nedd4 . Nedd4 chr9 72627390 72628209 INT_STITCHED_4636 2084 . Prtg Prtg chr9 72660060 72660935 INT_STITCHED_4637 1839 Prtg . Prtg chr9 72918450 72919308 INT_STITCHED_4639 2373 . Rab27a Rab27a chr9 75412496 75413425 INT_STITCHED_4648 2748 Tmod3 . Tmod3 chr9 77606686 77607650 INT_STITCHED_4652 2346 Gclc . Gclc chr9 77951768 77952528 INT_STITCHED_4654 8446 Ick, Fbxo9 . Fbxo9 chr9 78038277 78039230 INT_STITCHED_4656 1191 Gsta4 . Gsta4 chr9 88227178 88228053 INT_STITCHED_4678 2664 Nt5e . Nt5e chr9 88377528 88378586 INT_STITCHED_4680 2087 Syncrip . Syncrip chr9 97013591 97015267 INT_STITCHED_4696 251 Slc25a36 . Slc25a36 chr9 100540961 100541608 INT_STITCHED_4706 5773 Stag1 Nck1 Stag1 chr9 100934315 100942688 INT_STITCHED_4708 795 Pccb . Pccb chr9 102592120 102593562 INT_STITCHED_4714 366 . Amotl2 Amotl2 chr9 106069546 106074893 INT_STITCHED_4726 870 Wdr82 . Wdr82 chr9 107477688 107478518 INT_STITCHED_4729 1235 Hyal2, Nat6, . Hyal1 Hyal3, Hyal1 chr9 107496491 107497240 INT_STITCHED_4730 3614 Ifrd2, . BY080835 BY080835 chr9 107529104 107533461 INT_STITCHED_4731 483 Gnai2 BY080835, Gnai2 Sema3b, Gnai2 chr9 107579734 107580327 INT_STITCHED_4732 8441 . BY080835, Slc38a3 Sema3b, Slc38a3 chr9 108198631 108208673 INT_STITCHED_4735 642 Nicn1, Tcta, . Tcta Rhoa, Amt chr9 108424057 108425078 INT_STITCHED_4736 6827 Qrich1 . Qrich1 chr9 108469174 108470010 INT_STITCHED_4737 746 Ndufaf3, . Ndufaf3 Dalrd3, Mir425, Mir191, Impdh2 chr9 108556747 108557725 INT_STITCHED_4738 910 Arih2 . Arih2 chr9 109774888 109775365 INT_STITCHED_4742 6978 Cdc25a . Cde25a chr9 110562502 110563156 INT_STITCHED_4745 5313 Nbeal2,C . Ccdc12 cdc12 chr9 110647812 110648457 INT_STITCHED_4746 4458 Pth1r . Pth1r chr9 110757426 110757966 INT_STITCHED_4747 4546 Prss50 . Prss50 chr9 114493073 114494132 INT_STITCFIED_4767 342 . Trim71, Trim71 Ccr4, Cnot10 chr9 114549100 114549959 INT_STITCHED_4769 1830 Cnot10 . Cnot10 chr9 121898518 121899106 INT_STITCHED_4805 5244 C85492 . C85492 chr10 4521315 4524373 INT_STITCHED_4811 2104 Mtrfl1 . Mtrfl1 chr10 6056028 6057101 INT_STITCHED_4818 761 . Akap12 Akap12 chr10 6080029 6080762 INT_STITCHED_4819 917 Akap12 . Akap12 chr10 6096866 6104516 INT_STITCHED_4820 441 . Akap12 Akap12 chr10 8605895 8609821 INT_STITCHED_4831 1322 Sashl . Sashl chr10 12733586 12734303 INT_STITCHED_4846 5442 Sf3b5 . Sc3b5 chr10 14423031 14423523 INT_STITCHED_4852 7521 Vta1 . Vta1 chr10 18188738 18189638 INT_STITCHED_4868 3221 Nhsl1 . Nhsl1 chr10 19428463 19429212 INT_STITCHED_4875 6208 Il20ra . Il20ra chr10 19658492 19658963 INT_STITCHED_4878 7066 Map3k5 . Map3k5 chr10 21018761 21019274 INT_STITCHED_4887 8431 Hbsl1 . Hbsl1 chr10 21421393 21422103 INT_STITCHED_4889 1253 . Sgk1 Sgk1 chr10 21565286 21568461 INT_STITCHED_4892 286 . Sgk1 Sgk1 chr10 24310265 24311057 INT_STITCHED_4897 2376 Ctgf . Ctgf chr10 24545811 24555200 INT_STITCHED_4901 526 Enpp3 . Enpp3 chr10 24582734 24583438 INT_STITCHED_4902 5640 Med23 . Med23 chr10 33950012 33957066 INT_STITCHED_4929 283 . Dse, Bet31 Dse chr10 39338030 39338814 INT_STITCHED_4948 1945 Traf3ip2 . Traf3ip2 chr10 39455931 39456518 INT_STITCHED_4951 3274 Rev3l . Rev3l chr10 41186875 41187821 INT_STITCHED_4960 960 . Mical1 Mical1 chr10 41346832 41347467 INT_STITCHED_4962 5177 . Cd164 Cd164 chr10 43196881 43198135 INT_STITCHED_4973 840 Bend3 . Bend3 chr10 44792055 44792644 INT_STITCHED_4991 4429 Prep . Prep chr10 56093669 56096370 INT_STITCHED_5009 954 Gja1 . Gja1 chr10 57211848 57212434 INT_STITCHED_5011 4297 Hsf2 . Hsf2 chr10 60837711 60845392 INT_STITCHED_5034 833 X99384 Nodal X99384 chr10 60878292 60880002 INT_STITCHED_5035 307 . X99384 X99384 chr10 61695639 61705502 INT_STITCHED_5041 1103 Tspan15 . Tspan15 chr10 61976766 61977458 INT_STITCHED_5043 4198 Srgn . Srgn chr10 62699664 62700521 INT_STITCHED_5046 2504 Herc4 . Herc4 chr10 66465837 66467256 INT_STITCHED_5056 264 . Reep3 Reep3 chr10 69388191 69389259 INT_STITCHED_5073 2588 Ank3 . Ank3 chr10 69557563 69558392 INT_STITCHED_5074 1760 Ccdc6 . Ccdc6 chr10 69895948 69896630 INT_STITCHED_5079 5291 . Fam13c Fam13c chr10 70808586 70809333 INT_STITCHED_5083 4254 Cisd1, Ipmk . Cisd1 chr10 75491765 75492542 INT_STITCHED_5094 1070 Zfp280b . Zfp280b chr10 75902165 75902804 INT_STITCHED_5096 1995 Pcnt . Pcnt chr10 77065603 77066355 INT_STITCHED_5102 2639 Sumo3 . Sumo3 chr10 77500956 77501452 INT_STITCHED_5103 1526 Aire, Dnmt3l . Dnmt3l chr10 79135588 79136419 INT_STITCHED_5110 572 Gm16517 . Gm16517 chr10 80692540 80693324 INT_STITCHED_5115 2022 Zfr2, Atcay . Atcay chr10 82323925 82324687 INT_STITCHED_5120 3996 Txnrdl . Txnrdl chr10 82806815 82809352 INT_STITCHED_5121 1327 Slc41a2 . Slc41a2 chr10 84218273 84221859 INT_STITCHED_5131 1622 Rfx4 . Rfx4 chr10 84373188 84374377 INT_STITCHED_5135 1465 Ric8b Rfx4 Ric8b chr10 86247737 86248402 INT_STITCHED_5145 3820 Nt5dc3 . Nt5dc3 chr10 87323661 87324242 INT_STITCHED_5151 8413 Igf1 . Igf1 chr10 91625760 91626428 INT_STITCHED_5166 4875 Rmst Rms chr10 92628272 92629369 INT_STITCHED_5170 6413 Cdk17, . Mir1931 Mir1931 chr10 94877813 94878427 INT_STITCHED_5186 1768 Socs2 . Socs2 chr10 99484471 99485189 INT_STITCHED_5204 4932 Kitl . Kitl chr10 102831472 102832261 INT_STITCHED_5212 2315 Slc6a15 . Slc6a15 chr10 114819854 114820700 INT_STITCHED_5234 8036 Zfc3h1, . Zfc3h1 Thap2 che10 116589007 116589893 INT_STITCHED_5241 2171 Frs2 . Frs2 chr10 117140641 117141390 INT_STITCHED_5243 8406 Mdm2 . Mdm2 chr10 117285236 117286671 INT_STITCHED_5245 5005 Rap1b . Rap1b chr10 121179350 121180065 INT_STITCHED_5263 3080 BC048403 . BC048403 chr10 125407173 125407844 INT_STITCHED_5274 4971 Lrig3 . Lrig3 chr10 126707459 126707875 INT_STITCHED_5278 5620 Dctn2 . Dctn2 chr10 127027476 127027943 INT_STITCHED_5279 1610 . Lrp1 Lrp1 chr10 127531580 127532717 INT_STITCHED_5281 1409 Baz2a . Baz2a chr10 127806805 127807509 INT_STITCHED_5284 2080 Coq10a . Coq10a chr10 128068373 128069108 INT_STITCHED_5286 2913 Rps26 . Rps26 chr11 3189708 3193686 INT_STITCHED_5290 502 Patz1 Drg1 Patz1 chr11 4543384 4544389 INT_STITCHED_5303 4817 Ascc2 . Ascc2 chr11 4605024 4605900 INT_STITCHED_5305 5202 Zmat5, . Zmat5 Uqcr10 chr11 5602509 5603082 INT_STITCHED_5311 4735 Mrps24 . Mrps24 chr11 5640939 5641684 INT_STITCHED_5312 1772 Urgcp . Urgcp chr11 18925903 18926553 INT_STITCHED_5359 8097 . Meis1 Meis1 chr11 19817749 19818637 INT_STITCHED_5365 2246 Spred2 . Spred2 chr11 20094772 20095341 INT_STITCHED_5371 5514 Rab1 . Rab1 chr11 29922145 29922784 INT_STITCHED_5413 6619 Eml6 . Eml6 chr11 34215057 34215897 INT_STITCHED_5430 3638 Fam196b . Fam196b chr11 40550744 40551400 INT_STITCHED_5447 4727 Nudcd2, . Nudcd2 Hmmr chr11 43338652 43339165 INT_STITCHED_5452 6258 Ccnjl . Ccnjl chr11 43399014 43399833 INT_STITCHED_5453 3868 . Ccnjl Ccnjl chr11 45869858 45873818 INT_STITCHED_5465 1130 Adam19 . Adam19 chr11 51451223 51451993 INT_STITCHED_5482 848 Rmnd5b D930048N14Rik, Rmnd5b N4bp3 chr11 54672906 54673698 INT_STITCHED_5498 3249 Hint1, . Lyrm7 Lyrm7 chr11 59324891 59325529 INT_STITCHED_5512 5165 Zkscan17, . Zkscan17 4933439C10Rik chr11 59627660 59635535 INT_STITCHED_5513 2071 Flcn . Flcn chr11 60236311 60237216 INT_STITCHED_5515 6543 Atpaf2, . 4933439F18Rik 4933439F18Rik chr11 60590721 60591349 INT_STITCHED_5516 3272 Top3a, . Top3a Smcr8 chr11 60650172 60651011 INT_STITCHED_5517 3776 Dhrs7b . Dhrs7b chr11 60736253 60737190 INT_STITCHED_5519 1008 . Map2k3, Gm16516 Gm16516 chr11 60994880 60995724 INT_STITCHED_5521 3196 Usp22 . Usp22 chr11 61391409 61392089 INT_STITCHED_5527 7849 Epn2 . Epn2 chr11 62351245 62352154 INT_STITCHED_5534 2339 Cenpv . Cenpv chr11 62686433 62687279 INT_STITCHED_5535 1997 Fam18b . Fam18b chr11 62950261 62950815 INT_STITCHED_5538 7452 Pmp22 . Pmp22 chr11 69377638 69378461 INT_STITCHED_5563 3113 Efnb3 . Efnb3 chr11 69394651 69396118 INT_STITCHED_5564 602 Trp53, Dnahc2, Trp53 Wrap53 Atp1b2 chr11 74534022 74534794 INT_STITCHED_5581 3606 Pafah1b1 . Pafah1b1 chr11 77486774 77494239 INT_STITCHED_5595 593 Nufip2 . Nufip2 chr11 78060890 78061883 INT_STITCHED_5601 2175 Supt6h, . Supt6h Sdf2 chr11 79066770 79067524 INT_STITCHED_5610 3716 Wsb1 . Wsb1 chr11 79945260 79951952 INT_STITCHED_5618 259 1110002N22Rik . 1110002N22Rik chr11 79990875 79991582 INT_STITCHED_5619 1000 Rnf135 . Rnf135 chr11 80942931 80947956 INT_STITCHED_5623 1654 . Accn1 Accn1 chr11 82648830 82649486 INT_STITCHED_5636 8383 Rffl . Rffl chr11 85052297 85054262 INT_STITCHED_5646 4478 Appbp2, . D630032N06Rik D630032N06Rik chr11 86809492 86810234 INT_STITCHED_5657 8055 Ypel2 . Ypel2 chr11 87983937 87984484 INT_STITCHED_5660 5125 Cuedc1 . Cuedc1 chr11 88006524 88016104 INT_STITCHED_5661 1190 Mrps23 Vezf1 Mrps23 chr11 88718915 88724318 INT_STITCHED_5670 1418 Akap1 . Akap1 chr11 88829276 88830722 INT_STITCHED_5672 515 Coil, Coil, 2210409E12Rik 2210409E12Rik 2210409E12Rik chr11 89103298 89103997 INT_STITCFIED_5678 2377 . Nog Nog chr11 89857107 89857767 INT_STITCHED_5681 6616 Pctp . Pctp chr11 93749460 93750030 INT_STITCHED_5687 8380 Mbtd1, . Mbtd1 Utp18 chr11 95172573 95174382 INT_STITCHED_5689 796 Myst2 . Myst2 chr11 95841647 95842789 INT_STITCHED_5696 698 . Igf2bp1 Igf2bp1 chr11 95878892 95879756 INT_STITCHED_5697 1471 . Igf2bp1 Igf2bp1 chr11 95975203 95975967 INT_STITCHED_5698 5002 Calcoco2 , Calcoco2 chr11 96641262 96642250 INT_STITCHED_5703 4098 Snx11 . Snx11 chr11 96712000 96712739 INT_STITCHED_5705 2650 Copz2, . Copz2 Mir152 chr11 97053223 97053840 INT_STITCHED_5706 5798 Kpnb1 . Kpnb1 chr11 97428279 97440933 INT_STITCHED_5709 449 Srcin1 Srcin1 Srcin1 chr11 97486767 97487595 INT_STITCHED_5710 8378 E130012A19Rik . E130012A19Rik chr11 97638286 97638942 INT_STITCHED_5713 2574 Snora21, . 1700001P01Rik Rp123, 1700001P01Rik chr11 98062871 98063570 INT_STITCHED_5715 2004 Cdk12 . Cdk12 chr11 98653131 98654005 INT_STITCHED_5717 1984 Msl1 . Msl1 chr11 98787666 98788235 INT_STITCHED_5718 1642 . Rara Rara chr11 99105144 99105721 INT_STITCHED_5723 5192 Krt222 . Krt222 chr11 100394982 100396447 INT_STITCHED_5727 3839 Acly . Acly chr11 100477440 100478074 INT_STITCHED_5728 4810 Dnajc7, . Dnajc7 Nkiras2 chr11 101168796 101169594 INT_STITCHED_5732 5395 Becn1 . Becn1 chr11 101188000 101188651 INT_STITCHED_5733 5601 Aoc2 . Aoc2 chr11 101409700 101410324 INT_STITCHED_5735 3018 Nbr1, Brca1 . Brca1 chr11 101442692 101443650 INT_STITCHED_5736 1150 Tmem106a . Tmem106a chr11 102464622 102465176 INT_STITCHED_5744 3982 Fzd2 . Fzd2 chr11 102680774 102688178 INT_STITCHED_5745 573 Gjc1 . Gjc1 chr11 102973458 102974493 INT_STITCHED_5747 3140 Hexim1 . Hexim1 chr11 104461680 104462667 INT_STITCHED_5754 3299 . Itgb3 Itgb3 chr11 106130335 106130757 INT_STITCHED_5756 4137 Smarcd2 . Smarcd2 chr11 107372036 107379089 INT_STITCHED_5769 1159 . Helz Helz chr11 108285157 108286105 INT_STITCHED_5772 3390 Ccdc46 . Ccdc46 chr11 109212771 109222498 INT_STITCHED_5778 498 Gna13 . Gna13 chr11 109337038 109341696 INT_STITCHED_5779 2659 Slc16a6, . Slcl6a6 Arsg chr11 110904378 110905140 INT_STITCHED_5784 4199 . Kcnj2 Kcnj2 chr11 113570971 113572300 INT_STITCHED_5798 646 Cpsf41 . Cpsf41 chr11 116272666 116273421 INT_STITCHED_5813 3629 Rnf157 . Rnf157 chr11 116286146 116291508 INT_STITCHED_5814 242 Fam100b, Fam100b, Fam100b Gm7367 Gm7367 chr11 116447490 116448378 INT_STITCHED_5815 1674 Ube2o Rhbdf2, Ube2o Aanat chr11 117180985 117182314 INT_STITCHED_5821 683 . Sept9 9-Sep chr11 117736789 117737509 INT_STITCHED_5830 985 Tha1 Gm125 Tha1 81, Socs3 chr11 118335167 118335821 INT_STITCHED_5833 3791 Engase . Engase chr11 119256568 119257332 INT_STITCHED_5838 3429 Mir1932 . Mir1932 chr11 119798926 119799586 INT_STITCHED_5842 2594 Baiap2 . Baiap2 chr11 120009574 120010144 INT_STITCHED_5843 5089 Slc38a10 . Slc38a10 chr11 120092762 120093212 INT_STITCHED_5845 1725 Bahcc1 . Bahcc1 chr11 120638338 120641722 INT_STITCHED_5848 8042 Rfng, Gps1 Dcxr, Rac3, Rfng Lrrc45, Stra13, Cd7 chr11 120687588 120688365 INT_STITCHED_5850 2331 Fasn . Fasn chr12 3889637 3890588 INT_STITCHED_5856 1043 Dnmt3a . Dnmt3a chr12 8504710 8505271 INT_STITCHED_5867 3636 Rhob . Rhob chr12 8947875 8949112 INT_STITCHED_5868 1831 Matn3 . Matn3 chr12 12826439 12835796 INT_STITCHED_5877 291 . Mycn Mycn chr12 12882069 12897292 INT_STITCHED_5878 704 . Mycn Mycn chr12 12916267 12917170 INT_STITCHED_5879 619 . Mycn Mycn chr12 15821175 15834231 INT_STITCHED_5886 3248 Trib2 . Trib2 chr12 21424419 21425048 INT_STITCHED_5899 1820 Ywhaq . Ywhaq chr12 30624985 30625635 INT_STITCHED_5920 7091 Pxdn . Pxdn chr12 33509420 33509920 INT_STITCHED_5930 7423 Nampt . Nampt chr12 34111976 34112967 INT_STITCHED_5937 1469 Twistnb . Twistnb chr12 35730495 35731263 INT_STITCHED_5940 6653 Snx13 . Snx13 chr12 39505938 39511410 INT_STITCHED_5946 1065 Etv1 . Etv1 chr12 40724179 40725294 INT_STITCHED_5951 685 . Arl4a Arl4a chr12 53192336 53192990 INT_STITCHED_5981 4952 Nubpl . Nubpl chr12 56574184 56574829 INT_STITCHED_5999 1512 . Nfkbia Nfkbia chr12 57621203 57622656 INT_STITCHED_6005 3963 . Nkx2-9, Nkx2-9 Nkx2-1 chr12 70265691 70266182 INT_STITCHED_6029 4819 Rps29, Ppil5 . Ppil5 chr12 70831225 70831963 INT_STITCHED_6030 6534 L2hgdh, . Atp5s Atp5s chr12 73766180 73766775 INT_STITCHED_6045 4739 Dhrs7 . Dhs7 chr12 74186448 74187579 INT_STITCHED_6050 440 . Six4 Stx4 chr12 76765083 76765824 INT_STITCHED_6059 4579 Wdr89 . Wdr89 chr12 78065948 78066766 INT_STITCHED_6068 1575 Max . Max chr12 80129129 80136928 INT_STITCHED_6073 1017 Plekhh1 . Plekhh1 chr12 81212072 81218304 INT_STITCHED_6080 510 Zfp36l1 2310015A10Rik Zfp36l1 chr12 82022144 82022886 INT_STITCHED_6087 1355 1700052122Rik . 1700052122Rik chr12 85349930 85350505 INT_STITCHED_6099 3435 Acot1 . Acot1 chr12 85395735 85396391 INT_STITCHED_6101 7236 Acot3 . Acot3 chr12 85542980 85552631 INT_STITCHED_6102 547 . C130039016Rik C130039016Rik chr12 85959743 85966609 INT_STITCHED_6104 2233 Abcd4 . Abcd4 chr12 85981457 85981955 INT_STITCHED_6105 3978 7420416P09Rik . 7420416P09Rik chr12 86961855 86962511 INT_STITCHED_6108 1400 . Jdp2 Jdp2 chr12 88272118 88274195 INT_STITCHED_6119 243 . 2310044G17Rik 2310044G17Rik chr12 92821598 92822554 INT_STITCHED_6125 6873 Gtf2a1 . Gtf2a1 chr12 101575664 101576434 INT_STITCHED_6140 2502 . Calm1 Calm1 chr12 101958877 101959439 INT_STITCHED_6144 8355 Rps6ka5 . Rps6ka5 chr12 102234372 102235188 INT_STITCHED_6147 1248 . Ccdc88c, Ccdc88c Mir1190 chr12 102256843 102257522 INT_STITCHED_6148 4400 . Ccdc88c Ccdc88c chr12 103997082 103997697 INT_STITCHED_6153 1726 LOC100233175, . LOC100233175 Ubr7 chr12 106462467 106463587 INT_STITCHED_6165 1527 Tcl1 . Tcl1 chr12 107250243 107250762 INT_STITCHED_6169 6539 Vrk1 . Vrk1 chr12 111940531 111941453 INT_STITCHED_6190 295 Hsp90aa1 . Hsp90aa1 chr12 112075298 112076240 INT_STITCHED_6192 273 Stk30 . Stk30 chr12 112908378 112914863 INT_STITCHED_6195 705 Ckb, . Ckb Trmt61a chr12 117645942 117646660 INT_STITCHED_6200 8345 Ncapg2, . Ncapg2 D430020J02Rik chr12 120476393 120476813 INT_STITCHED_6215 7174 Itgb8 . Itgb8 chr13 17791823 17792717 INT_STITCHED_6256 6230 5033411D12Rik, . 2810021B07Rik 2810021B07Rik chr13 19720204 19721138 INT_STITCHED_6261 3029 Sfrp4 . Sfrp4 chr13 20132694 20133451 INT_STITCHED_6264 3726 . Elmo1 Elmo1 chr13 20275154 20275936 INT_STITCHED_6267 1192 Elmo1 Txndc3 Elmo1 chr13 21819716 21820326 INT_STITCHED_6274 3648 Hist1h2bm . Hist1h2bm chr13 21840858 21841391 INT_STITCHED_6275 4915 Hist1h2bn, . Hist1h4k Hist1h2ak, Hist1h4k chr13 21877978 21883093 INT_STITCHED_6276 351 Hist1h2bp, . Hist1h2kbp Hist1h2an, Hist1h3i, Hist1h1b chr13 23583742 23584526 INT_STITCHED_6279 3060 Btn2a2 . Btn2a2 chr13 23678018 23687970 INT_STITCHED_6280 344 Hist1h4d . Hist1h4d chr13 23833718 23834547 INT_STITCHED_6281 391 Hist1h1c, . Hist1h3c Hist1h3c, Hist1h2bb chr13 24929573 24930214 INT_STITCHED_6284 6023 Tdp2, . Tdp2 Acot13 chr13 25366681 25367257 INT_STITCHED_6287 3396 Nrsn1 . Nrsn1 chr13 34130311 34131047 INT_STITCHED_6307 6483 Bph1 . Bph1 chr13 34201201 34202268 INT_STITCHED_6308 434 . Tubb2b Tubb2b chr13 34222647 34226305 INT_STITCHED_6309 622 Tubb2b Tubb2a Tubb2b chr13 35829899 35831775 INT_STITCHED_6317 1240 Cdyl . Cdyl chr13 40959133 40964971 INT_STITCHED_6339 319 Gcnt2 . Gcnt2 chr13 41012552 41013182 INT_STITCHED_6340 1683 Gcnt2 . Gcnt2 chr13 43709828 43710545 INT_STITCHED_6355 5257 Rnf182 . Rnf182 chr13 44800270 44801323 INT_STITCHED_6366 461 . Jarid2 Jarid2 chr13 44817274 44824484 INT_STITCHED_6367 581 Jarid2 . Jarid2 chr13 49276801 49277722 INT_STITCHED_6386 2201 Ninj1 . Ninj1 chr13 51940931 51942277 INT_STITCHED_6396 523 Gadd45g . Gadd45g chr13 52015693 52016983 INT_STITCHED_6398 674 . Gadd45g Gadd45g chr13 52347463 52348186 INT_STITCHED_6401 2330 . Gadd45g, Diras2 Diras2 chr13 53329991 53330847 INT_STITCHED_6409 1992 . Ror2 Ror2 chr13 54162877 54163531 INT_STITCHED_6412 6319 Sfxn1 . Sfxn1 chr13 54884318 54885163 INT_STITCHED_6417 3296 Tspan17 . Tspan17 chr13 56244196 56245355 INT_STITCHED_6422 854 . H2afy H2afy chr13 56713179 56714077 INT_STITCHED_6427 2610 Tgfbi . Tgfbi chr13 59690911 59691486 INT_STITCHED_6440 7090 Naa35 . Naa35 chr13 60272270 60272721 INT_STITCHED_6442 5894 Gas1 . Gas1 chr13 60728970 60729626 INT_STITCHED_6443 2400 . Dapk1 Dapk1 chr13 63629801 63643443 INT_STITCHED_6456 406 . Ptch1 Ptch1 chr13 63670190 63671046 INT_STITCHED_6457 2439 Ptch1 . Ptch1 chr13 67945216 67959075 INT_STITCHED_6469 465 BC048507 BC048507 BC048507 chr13 73919814 73920680 INT_STITCHED_6489 2743 . Slc12a7 Slc12a7 chr13 81025875 81025976 INT_STITCHED_6503 7815 Arrdc3 . Arrdc3 chr13 81795260 81796035 INT_STITCHED_6504 5336 Lysmd3 . Lysmd3 chr13 91064620 91065354 INT_STITCHED_6526 3284 Rps23, . Rps23 Gm15450 chr13 93381777 93382383 INT_STITCHED_6530 7201 Scrinc5 . Serinc5 chr13 95135009 95135833 INT_STITCHED_6533 2985 Ap3b1 . Ap3b1 chr13 97443596 97446190 INT_STITCHED_6552 2544 Hmgcr . Hmgcr chr13 97836707 97837573 INT_STITCHED_6553 1068 Fam169a . Fam169a chr13 97966165 97977878 INT_STITCHED_6555 616 Hexb Hexb Hexb chr13 98014519 98015236 INT_STITCHED_6556 3643 Enc1 . Enc1 chr13 98087481 98090981 INT_STITCHED_6558 1579 . Enc1 Enc1 chr13 98264472 98265266 INT_STITCHED_6560 2674 . Enc1 Enc1 chr13 98357754 98358697 INT_STITCHED_6562 669 . Enc1 Enc1 chr13 100284416 100285117 INT_STITCHED_6580 4686 Mtap1b . Mtap1b chr13 110565130 110569253 INT_STITCHED_6617 879 . Mir1904 Mir1904 chr13 113230066 113231347 INT_STITCHED_6629 1467 . Il6st Il6st chr13 113252258 113253581 INT_STITCHED_6630 1221 Il6st . Il6st chr13 114397781 114409794 INT_STITCHED_6636 433 Snx18 Snx18 Snx18 chr13 115890657 115891471 INT_STITCHED_6647 5940 Itga1 . Itga1 chr13 118004296 118004900 INT_STITCHED_6650 3770 Emb . Emb chr14 9051276 9051941 INT_STITCHED_6658 4216 Kctd6 . Kctd6 chr14 19159762 19160472 INT_STITCHED_6696 3410 Ube2e1 . Ube2e1 chr14 21296378 21296820 INT_STITCHED_6706 5511 Anxa7 . Anxa7 chr14 26137169 26138011 INT_STITCHED_6720 1523 . Zmiz1 Zmiz1 chr14 26410307 26411097 INT_STITCHED_6722 496 4931406H21Rik . 4931406H21Rik chr14 31470534 31471189 INT_STITCHED_6747 5925 Rft1 . Rft1 chr14 33667117 33667576 INT_STITCHED_6755 5182 E130203B14Rik . E130203B14Rik chr14 35125619 35137157 INT_STITCHED_6757 918 Glud1, . Glud1 Fam35a chr14 37908776 37909202 INT_STITCHED_6767 5315 Cdhr1 . Cdhr1 chr14 48192256 48193061 INT_STITCHED_6783 724 Atg14 . Atg14 chr14 51402468 51403045 INT_STITCHED_6800 5810 Ttc5 . Ttc5 chr14 51558001 51558879 INT_STITCHED_6802 3169 Pnp . Pnp chr14 52505644 52512650 INT_STITCHED_6806 2589 Mett11d1 . Mett11d1 chr14 52685699 52686443 INT_STITCHED_6807 1423 Snord58b . Snord58b chr14 52903759 52904402 INT_STITCHED_6808 6169 Rab2b, . Rab2b Tox4 chr14 55034351 55034932 INT_STITCHED_6813 1230 Slc7a7 . Slc7a7 chr14 56453893 56454720 INT_STITCHED_6820 1918 . Nfatc4 Nfatc4 chr14 58148750 58156587 INT_STITCHED_6825 353 Il17d . Il17d chr14 58351276 58352213 INT_STITCHED_6826 4644 . Lats2 Lats2 chr14 61274229 61274887 INT_STITCHED_6840 3553 . Spata13 Spata13 chr14 61752861 61757994 INT_STITCHED_6847 1431 Sacs . Sacs chr14 62221688 62222494 INT_STITCHED_6848 2608 Trim13 . Trim13 chr14 62950025 62953666 INT_STITCHED_6853 597 Rnaseh2b Gucy1b2 Rnaseh2b chr14 66422334 66422947 INT_STITCHED_6868 7006 Pbk . Pbk chr14 66741005 66742036 INT_STITCHED_6870 2212 Ephx2 . Ephx2 chr14 66902737 66903245 INT_STITCHED_6871 7981 Ptk2b . Ptk2b chr14 68506004 68512434 INT_STITCHED_6878 770 . Dock5 Dock5 chr14 68554515 68560104 INT_STITCHED_6879 1749 Dock5 . Dock5 chr14 70751362 70752223 INT_STITCHED_6886 1690 Slc39a14 . Slc39a14 chr14 73637897 73638790 INT_STITCHED_6892 2422 Lpar6 . Lpar6 chr14 76958882 76959494 INT_STITCHED_6905 4979 Serp2 . Serp2 chr14 78937419 78938329 INT_STITCHED_6918 3162 Akap11 . Akap11 chr14 79121670 79134144 INT_STITCHED_6920 751 Dgkh . Dgkh chr14 79964561 79965081 INT_STITCHED_6925 3530 . Sugt1 Sugt1 chr14 79983072 79983942 INT_STITCHED_6926 3473 Sugt1 . Sugt1 chr14 99438364 99439107 INT_STITCHED_6951 2329 Mzt1, . Mzt1 6720463M24Rik chr14 103474469 103477990 INT_STITCHED_6969 6686 Cln5 . Cln5 chr14 105572867 105573451 INT_STITCHED_6977 7790 Rbm26 . Rbm26 chr14 106319658 106320994 INT_STITCHED_6983 663 . Spry2 Spry2 chr14 117326693 117327070 INT_STITCHED_6995 6044 Gpc6 . Gpc6 chr14 118629366 118630181 INT_STITCHED_6999 5217 Sox21 . Sox21 chr14 119332449 119333029 INT_STITCHED_7007 4788 Dnajc3 . Dnajc3 chr14 120883645 120884276 INT_STITCHED_7011 8270 Rap2a . Rap2a chr14 121905233 121906137 INT_STITCHED_7018 716 Slc15a1 . Slc15a1 chr15 7065153 7068694 INT_STITCHED_7046 435 . Lifr Lifr chr15 9064661 9065183 INT_STITCHED_7054 1757 Skp2, Tmbrd2 . Skp2 chr15 10615155 10617848 INT_STITCHED_7060 687 . Rai14 Rai14 chr15 10640824 10653875 INT_STITCHED_7061 331 Rai14 Rai14 Rai14 chr15 10906708 10907428 INT_STITCHED_7063 6029 Amacr . Amacr chr15 12045435 12046215 INT_STITCHED_7072 2830 Zfr . Zfr chr15 12133202 12134066 INT_STITCHED_7073 1153 Mtmr12 . Mtmr12 chr15 12243117 12252382 INT_STITCHED_7075 4108 Golph3 . Golph3 chr15 18748130 18748646 INT_STITCHED_7092 3781 Cdh10 . Cdh10 chr15 28000620 28001311 INT_STITCHED_7111 2701 . Trio Trio chr15 36941214 36941629 INT_STITCHED_7133 3228 Zfp706 . Zfp706 chr15 37989429 38008159 INT_STITCHED_7140 718 Ubr5 Ubr5 Ubr5 chr15 53173777 53175470 INT_STITCHED_7170 2943 Ext1 . Ext1 chr15 54746572 54747189 INT_STITCHED_7173 7556 Enpp2 . Enpp2 chr15 55095920 55100307 INT_STITCHED_7175 571 . Depdc6 Depdc6 chr15 56573900 56575358 INT_STITCHED_7180 1521 . Has2as, Has2 Has2 chr15 58052823 58053270 INT_STITCHED_7184 4922 Fbxo32 . Fbxo32 chr15 58244484 58245397 INT_STITCHED_7186 2649 D15Ertd621e . D15Ertd621e chr15 58901790 58915123 INT_STITCHED_7187 323 Mtss1 . Mtss1 chr15 61810188 61811058 INT_STITCHED_7200 3145 Myc . Myc chr15 61841217 61844889 INT_STITCHED_7201 648 . Myc Myc chr15 68752023 68752528 INT_STITCHED_7219 7222 Khdrbs3 . Khdrbs3 chr15 73013516 73014184 INT_STITCHED_7224 1136 Eif2c2 Kcnk9 Eif2c2 chr15 75708006 75732455 INT_STITCHED_7240 354 Naprt1 Ze3h3, Pycrl Naprt1 chr15 76909283 76909985 INT_STITCHED_7245 7260 . Rbm9 Rbm9 chr15 77678011 77678785 INT_STITCHED_7249 2418 Myh9 . Myh9 chr15 78726841 78727700 INT_STITCHED_7252 6124 Sh3bp1 . Sh3bp1 chr15 79278426 79279059 INT_STITCHED_7254 5952 Csnk1e . Csnk1e chr15 81530381 81531523 INT_STITCHED_7267 1732 Chadl . Chadl chr15 81560234 81560989 INT_STITCHED_7268 1988 Rangap1 . Rangap1 chr15 82050108 82060103 INT_STITCHED_7269 965 Tnfrsf13c . Tnfrsf13c chr15 84016374 84020249 INT_STITCHED_7275 763 Samm50 . Samm50 chr15 85668308 85668848 INT_STITCHED_7280 8064 Ttc38 . Ttc38 chr15 85696253 85696964 INT_STITCHED_7281 1767 Gtse1 . Gtse1 chr15 89308072 89308194 INT_STITCHED_7289 3434 Arsa . Arsa chr15 90886302 90887037 INT_STITCHED_7294 2964 Kif21aa . Kif21a chr15 93227987 93228712 INT_STITCHED_7300 3529 Pphln1, Zcrb1 . Pphln1 chr15 95618532 95618978 INT_STITCHED_7305 8246 Ano6 . Ano6 chr15 96009647 96010368 INT_STITCHED_7308 3414 Gm4371 . Gm4371 chr15 96532896 96533663 INT_STITCHED_7314 2240 Slc38a2 . Slc38a2 chr15 97659779 97660356 INT_STITCHED_7319 1887 Hdac7 . Hdac7 chr15 99702760 99705639 INT_STITCHED_7327 425 Lima1 . Lima1 chr15 99871865 99872478 INT_STITCHED_7329 5280 Dip2b . Dip2b chr15 100304382 100305176 INT_STITCHED_7332 1241 Letmd1 . Letmd1 chr15 101107344 101108241 INT_STITCHED_7336 865 9430023L20Rik 9430023L20Rik 9430023L20Rik chr15 102044350 102045008 INT_STITCHED_7337 1330 Zfp740 . Zfp740 chr15 102073324 102074272 INT_STITCHED_7338 421 Rarg Itgb7, Rarg Mfsd5, Rarg chr16 3849599 3850539 INT_STITCHED_7344 4390 Zfp174 . Zfp174 chr16 5252339 5252888 INT_STITCHED_7349 4879 Fam86 . Fam86 chr16 11260700 11261095 INT_STITCHED_7374 5533 Gspt1, . Mir1945 Mir1945 chr16 13785839 13786611 INT_STITCHED_7389 2293 Rrn3 . Rrn3 chr16 15587600 15588338 INT_STITCHED_7394 5959 Ube2v2 . Ube2v2 chr16 16302093 16302827 INT_STITCHED_7399 3684 Yars2 . Yars2 chr16 16825494 16826238 INT_STITCHED_7401 4532 Spag6 . Spag6 chr16 17928738 17929621 INT_STITCHED_7404 2773 Slc25a1 Dgcr14, Sle25a1 Gsc2 chr16 18242932 18243570 INT_STITCHED_7405 4927 Ranbp1, . Ranbp1 Trmt2a chr16 21995128 21996129 INT_ST1TCHED_7422 1389 Liph . Liph chr16 22015572 22016286 INT_STITCHED_7423 3870 Senp2 . Senp2 chr16 22139712 22161378 INT_STITCHED_7425 750 Igf2bp2 . Igf2bp2 chr16 22441980 22442886 INT_STITCHED_7428 4560 Etv5 . Etv5 chr16 24443296 24444024 INT_STITCHED_7439 4206 Lpp . Lpp chr16 30062920 30063517 INT_STITCHED_7457 379 Hes1 4632428C04Rik Hes1 chr16 30280722 30286306 INT_STITCHED_7459 799 Lrrc15 . Lrrc15 chr16 33178393 33179116 INT_STITCHED_7474 2437 Osbpl11 . Osbpl11 chr16 33246666 33247168 INT_STITCHED_7475 3771 Snx4 . Snx4 chr16 33379458 33380156 INT_STITCHED_7476 2939 Zfp148 . Zfp148 chr16 34692943 34693565 INT_STITCHED_7487 7029 Ccdc14 . Ccdc14 chr16 35966441 35966967 INT_STITCHED_7498 4502 . Parp9, Dtx31 Dtx31 chr16 36069406 36070168 INT_STITCHED_7499 4226 Fam162a, . Fam162a Ccdc58 chr16 36821606 36822164 INT_STITCHED_7504 5866 Iqcb1, Eaf2 . Eaf2 chr16 38558387 38558980 INT_STITCHED_7510 553 Tmem39a . Tmem39a chr16 45726028 45726467 INT_STITCHED_7533 5076 Tagln3 . Tagln3 chr16 46500728 46501425 INT_STITCHED_7535 2532 Pvrl3 . Pvrl3 chr16 48283498 4828425 INT_STITCHED_7537 4304 Dppa4 . Dppa4 chr16 48303474 48311051 INT_STITCHED_7538 424 Dppa2 . Dppa2 chr16 49861220 49862107 INT_STITCHED_7545 6187 Cd47 . Cd47 chr16 59643496 59644072 INT_STITCHED_7559 6185 Arl6 . Arl6 chr16 64766788 64767304 INT_STITCHED_7563 3850 4930453N24Rik . 4930453N24Rik chr16 78573987 78574492 INT_STITCHED_7592 6130 D16Ertd472e . D16Ertd472e chr16 84825000 84825796 INT_STITCHED_7598 6321 LOC654426 . LOC654426 chr16 90283267 90283824 INT_STITCHED_7605 4518 Srsf15 . Srsf15 chr16 91379084 91379709 INT_STITCHED_7614 5871 Ifnar2 . Ifnar2 chr16 91480485 91481228 INT_STITCHED_7616 3701 Ifna1 . Ifnar1 chr16 93826367 93827291 INT_STITCHED_7625 1443 Morc3 . Morc3 chr16 96304699 96305588 INT_STITCFIED_7631 500 Brwd1 . Brwd1 chr17 3551086 3551760 INT_STITCHED_7642 6038 Tfb1m . Tfb1m chr17 5407856 5417145 INT_STITCHED_7655 1717 Ldhal6b . Ldhal6b chr17 5490301 5490994 INT_STITCHED_7656 6367 Zdhhc14 . Zdhhc14 chr17 8568963 8569332 INT_STITCHED_7669 7541 T2 . T2 chr17 10527703 10528580 INT_STITCHED_7679 1195 . Qk Qk chr17 10693553 10694165 INT_STITCIIED_7683 2446 . Qk Qk chr17 14336522 14337258 INT_STITCHED_7693 3352 Dact2 . Dact2 chr17 14829950 14831243 INT_STITCHED_7696 2466 Thbs2 . Thbs2 chr17 15326610 15327365 INT_STITCHED_7697 2593 . Dll1 Dll1 chr17 15384508 15385475 INT_STITCHED_7699 733 . Dll1 Dll1 chr17 15513799 15519743 INT_STITCHED_7700 994 Dll1 Dll1 Dll1 chr17 17749211 17749858 INT_STITCHED_7709 5200 . Lnpep Lnpep chr17 23739864 23740605 INT_STITCHED_7716 2010 Zfp13, . Zscan10 Zscan10 chr17 23780427 23780792 INT_STITCHED_7718 6220 Mmp25 . Mmp25 chr17 23864226 23864239 INT_STITCHED_7720 8089 Pkmyt1 . Pkmyt1 chr17 23926672 23927280 INT_STITCHED_7721 3044 Flywch2 . Flywch2 chr17 24270829 24277012 INT_STITCHED_7722 3300 Pdpk1 . Pdpk1 chr17 24339885 24340488 INT_STITCHED_7723 2003 Ntn3 . Ntn3 chr17 25891931 25892657 INT_STITCHED_7727 8210 . Narfl Narfl chr17 27638391 27639320 INT_STITCHED_7735 2037 Grm4 . Grm4 chr17 28317168 28317281 INT_STITCHED_7740 8206 Zfp523 . Zfp523 chr17 29144582 29145786 INT_STITCHED_7744 843 Stk38 . Stk38 chr17 29631024 29631722 INT_STITCHED_7754 2521 Pim1 . Pim1 chr17 31433655 31445349 INT_STITCHED_7763 393 Slc37a1 Slc37a1 Slc37a1 chr17 32330938 32331519 INT_STITCHED_7769 6586 Ephx3 . Ephx3 chr17 33493774 33494196 INT_STITCHED_7774 7483 Zfp81 . Zfp81 chr17 34029161 34029875 INT_STITCHED_7777 2571 Kifc1 . Kifc1 chr17 35029917 35030731 INT_STITCHED_7781 4836 Ehmt2, . Zbtb12 Zbtb12 chr17 35087242 35087957 INT_STITCHED_7782 3133 Snord52, . Snord52 1110038B12Rik chr17 35201745 35214088 INT_STITCHED_7783 489 Ly6g6c, G6b, Ddah2, Ly6g6c AU023871, Ly6g6c, G6b, Ddah2, AU023871, Ly6g6e, Ly6g6e, Ly6g6d Ly6g6d chr17 36969445 36981968 INT_STITCHED_7790 811 Trim26 . Trim26 chr17 43010751 43011486 INT_STITCHED_7803 7133 Cd2ap . Cd2ap chr17 45743747 45744742 INT_STITCHED_7814 249 Gm7325 Gm7325, Gm7325 Slc29a1 chr17 45743747 45767400 INT_STITCHED_7815 . Gm7325 Gm7325 chr17 46134937 46135825 INT_STITCHED_7817 2549 . Vegfa Vegfa chr17 46929748 46930535 INT_STITCHED_7819 1600 . Rpl711 Rpl711 chr17 47702974 47709143 INT_STITCHED_7823 233 . Ccnd3 Ccnd3 chr17 47876080 47877026 INT_STITCHED_7825 668 . Frs3 Frs3 chr17 47925179 47925764 INT_STITCHED_7826 3923 Tcfeb . Taal chr17 48013535 48035748 INT_STITCHED_7828 415 . Foxp4 Foxp4 chr17 48112639 48113467 INT_STITCHED_7830 1618 . Foxp4 Foxp4 chr17 53690666 53701713 INT_STITCHED_7849 516 Kat2b . Kat2b chr17 56437658 56438221 INT_STITCHED_7852 8198 Arrdc5, . Arrdc5 Uhrf1 chr17 56972466 56973551 INT_STITCHED_7853 1996 Rfx2 . Rfx2 chr17 57008637 57009589 INT_STITCHED_7854 1483 1700061G19Rik 1700061G19Rik chr17 66305463 66305913 INT_STITCHED_7870 4767 Twsg1 . Twsg1 chr17 66453333 66453853 INT_STITCHED_7871 4415 Ndufv2 . Ndufv2 chr17 68041107 68061143 INT_STITCHED_7877 468 Lama1 . Lama1 chr17 68353194 68354191 INT_STITCHED_7878 2835 Arhgap28 . Arhgap28 chr17 74927087 74927097 INT_STITCHED_7897 8063 Birc6 . Birc6 chr17 75956321 75956983 INT_STITCHED_7905 5048 Fam98a . Fam98a chr17 79313190 79313799 INT_STITCHED_7912 1560 1110001A16Rik . 1110001A16Rik chr17 81128692 81129358 INT_STITCHED_7931 6152 Map4k3 . Map4k3 chr17 84582744 84583323 INT_STITCHED_7948 1781 Zfp36l2 Zfp36l2 Zfp36l2 chr17 86535700 86548495 INT_STITCHED_7964 2602 Srbd1 . Srbd1 chr17 87930591 87931316 INT_STITCHED_7969 1832 . Calm2 Calm2 chr17 88076955 88077637 INT_STITCHED_7971 5992 Msh2 . Msh2 chr17 88372701 88373685 INT_STITCHED_7972 900 Msh6 . Msh6 chr18 3385402 3385870 INT_STITCHED_7995 5889 Cul2 . Cul2 chr18 5163169 5163726 INT_STITCHED_8001 1733 . Zfp438 Zfp438 chr18 6516515 6517140 INT_STITCHED_8006 5074 Epc1 . Epc1 chr18 9214813 9216976 INT_STITCHED_8012 8186 Fzd8 . Fzd8 chr18 12002313 12002823 INT_STITCHED_8021 6352 Cables1, . Mir1901 Mir1901 chr18 12397312 12398585 INT_STITCHED_8024 2342 Npc1 . Npc1 chr18 12797614 12797946 INT_STITCHED_8029 7046 Ttc39c . Ttc39c chr18 14832586 14835577 INT_STITCHED_8038 2705 Ss18 . 5s18 chr18 20899101 20900111 INT_STITCHED_8051 1742 B4galt6 . B4galt6 chr18 21101897 21102870 INT_STITCHED_8053 899 Rnf125 . Rnf125 chr18 24151920 24152681 INT_STITCHED_8065 3525 Zfp35 . Zfp35 chr18 33621690 33622128 INT_STITCHED_8099 7581 D0H4S114 . D0H4S114 chr18 34109932 34110743 INT_STITCHED_8104 1197 . Epb4.1l4a Epb4.1l4a chr18 34157592 34158493 INT_STITCHED_8106 1702 . Epb4.1l4a Epb4.1l4a chr18 34701440 34715289 INT_STITCHED_8109 1027 Wnt8a Wnt8a Wnt8a chr18 34884236 34884615 INT_STITCHED_8111 4424 Gfra3 . Gfra3 chr18 34937293 34938906 INT_STITCHED_8112 1343 Kdm3b . Kdm3b chr18 35982138 35983371 INT_STITCHED_8122 717 Cxxc5 Cxxc5 Cxxc5 chr18 36924103 36924650 INT_STITCHED_8127 4027 Wdr55, . Dnd1 Dnd1 chr18 37892904 37893442 INT_STITCHED_8128 5966 Pcdhgb5, . Pcdhgb5 Pcdhga9 chr18 37911821 37912317 INT_STITCHED_8129 7509 Pcdhga11 . Pcdhga11 chr18 37931149 37931649 INT_STITCHED_8130 2988 Pcdhga12 Pcdhgc3 Pcdhga12 chr18 38000290 38000857 INT_STITCHED_8131 3762 . Pcdhgc3, Pcdhgc5 Pcdhgc5, Pcdhga12, Pcdhgb8 chr18 38092039 38092926 INT_STITCHED_8132 1852 Diap1 . Diap1 chr18 42432273 42432907 INT_STITCHED_8152 8174 Rbm27, . Rbm27 Gm4013 chr18 44538369 44547262 INT_STITCHED_8160 8173 Dcp2 . Dcp2 chr18 47518017 47518632 INT_STITCHED_8170 3236 . Sema6a Sema6a chr18 47652330 47656137 INT_STITCHED_8172 1172 . Sema6a Sema6a chr18 49992787 49993420 INT_STITCHED_8179 8172 Dmxl1 . Dmxl1 chr18 53570940 53571612 INT_STITCHED_8184 4918 Ppic . Ppic chr18 58016521 58042474 INT_STITCHED_8201 1921 Slc12q2 . Slc12q2 chr18 61194178 61196405 INT_STITCHED_8207 1611 . Slc6a7 Slc6a7 chr18 65575946 65587598 INT_STITCHED_8222 1816 Malt1 . Malt1 chr18 65737262 65738119 INT_STITCHED_8223 2710 Zfp532 . Zfp532 chr18 66620651 66621456 INT_STITCHED_8233 2103 Pmaip1 . Pmaip1 chr18 74223279 74224086 INT_STITCHED_8255 2698 Mapk4 . Mapk4 chr18 77799062 77800652 INT_STITCHED_8272 446 Rnf165 . Rnf165 chr18 77947287 77947954 INT_STITCHED_8273 4453 8030462N17Rik, . 8030462N17Rik 4930465K10Rik chr18 79302745 79303389 INT_STITCHED_8281 2887 Setbp1 . Setbp1 chr18 80345132 80345668 INT_STITCHED_8285 4859 Adnp2 . Adnp2 chr18 83085081 83085678 INT_STITCHED_8304 5214 Zfp516, . Zfp516 4930592I03Rik chr18 85101655 85104293 INT_STITCHED_8309 369 Fbxo15 . Fbxo15 chr19 3578494 3579148 INT_STITCHED_8314 5749 Ppp6r3 . Ppp6r3 chr19 4809961 4810938 INT_STITCHED_8317 1591 Rbm14 Rbm4b Rbm14 chr19 4849752 4850334 INT_STITCHED_8318 2176 Ctsf . Ctsf chr19 5362176 5362769 INT_STITCHED_8321 5559 Eiflad, . Banf1 Banf1 chr19 5806301 5807102 INT_STITCHED_8323 567 Malat1 Neat1 Malat1 chr19 6008924 6009669 INT_STITCHED_8325 2365 Capn1 . Capn1 chr19 7556157 7556974 INT_STITCHED_8330 7656 Rtn3 . Rtn3 chr19 10750948 10751863 INT_STITCHED_8339 5044 Pga5 . Pga5 chr19 10909944 10910853 INT_STITCHED_8342 3107 Slc15a3 . Slc15a3 chr19 11897650 11898585 INT_STITCHED_8348 4958 Stx3 . Stx3 chr19 23226190 23228627 INT_STITCHED_8387 340 Mir1192 Klf9 Mir1192 chr19 24625504 24626811 INT_STITCHED_8395 5338 Pip5k1b . Pip5k1b chr19 30019855 30020504 INT_STITCHED_8420 4142 Il33 . Il33 chr19 30103198 30104145 INT_STITCHED_8422 8079 Uhrf2 . Uhrf2 chr19 34270171 34270617 INT_STITCHED_8437 4678 Stambpl1 . Stambpl1 chr19 38110109 38124425 INT_STITCHED_8451 1141 Myof, . Myof Cep55 chr19 40335693 40347774 INT_STITCHED_8457 575 Pdlim1 . Pdlim1 chr19 41340652 41341549 INT_STITCHED_8462 2243 Tm9sf3 . Tm9sf3 chr19 41924877 41928541 INT_STITCHED_8467 4990 Frat2 . Frat2 chr19 42210160 42211146 INT_STITCHED_8468 381 . Avpi1 Avpi1 chr19 44336251 44340919 INT_STITCHED_8482 397 . Scd2 Scd2 chr19 45431191 45431778 INT_STITCHED_8492 4657 Btrc . Btrc chr19 46111427 46112378 INT_STITCHED_8495 1345 Ldb1 Ldb1, Ldb1 Nolc1 chr19 46147545 46148245 INT_STITCHED_8496 2738 Nolc1 . Nolc1 chr19 46571486 46579213 INT_STITCHED_8497 398 Trim8 . Trim8 chr19 47062698 47063420 INT_STITCHED_8499 2624 . Cnnm2, Nt5c2 Nt5c2, Ina chr19 47524932 47525874 INT_STITCHED_8502 923 . Sh3pxd2a Sh3pxd2a chr19 55810476 55811196 INT_STITCHED_8528 5265 Tcf712 Tcf712 Tcf712 chr19 57440147 57441699 INT_STITCHED_8534 1163 Fam160b1 . Fam160b1 chrX 7341901 7342556 INT_STITCHED_8551 1800 Tcfe3 . Tcfe3 chrX 7504022 7504775 INT_STITCHED_8553 2401 Eras . Eras chrX 7783981 7797322 INT_STITCHED_8558 902 Porcn . Porcn chrX 11585060 11585603 INT_STITCHED_8566 6900 . Bcor Bcor chrX 11650689 11656529 INT_STITCHED_8568 2596 Bcor . Bcor chrX 12336063 12336542 INT_STITCHED_8571 8138 Med14 . Med14 chrX 12623919 12624670 INT_STITCHED_8574 1251 . Usp9x Usp9x chrX 17148568 17149028 INT_STITCHED_8579 2968 Fundc1 . Fundc1 chrX 20450222 20452884 INT_STITCHED_8589 1414 Timp1 . Timp1 chrX 20639136 20640111 INT_STITCHED_8591 4023 Zfp182 . Zfp182 chrX 34345348 34357788 INT_STITCHED_8599 417 . Slc25a5 Slc25a5 chrX 45948994 45949828 INT_STITCHED_8615 5413 Zfp280c . Zfp280c chrX 49037620 49038464 INT_STITCHED_8621 4650 Hs6st2 . Hs6st2 chrX 49516745 49521331 INT_STITCHED_8623 1198 Gpc4 . Gpc4 chrX 49542203 49542936 INT_STITCHED_8624 1909 . Gpc4 Gpc4 chrX 68472013 68472518 INT_STITCHED_8648 6076 Mtm1 . Mtm1 chrX 68812416 68812867 INT_STITCHED_8650 6998 Hmgb3 . Hmgb3 chrX 71062069 71066856 INT_STITCHED_8654 1325 Pdzd4 . Pdzd4 chrX 74758128 74771144 INT_STITCHED_8657 2215 Tbl1x . Tbl1x chrX 83432509 83439416 INT_STITCHED_8673 699 Nr0b1 . Nr0b1 chrX 90909066 90918687 INT_STITCHED_8678 2200 Pcyt1b . Pcyt1b chrX 98279269 98280110 INT_STITCHED_8695 2327 Slc7a3 . Slc7a3 chrX 98832291 98835492 INT_STITCFIED_8698 888 Ogt . Ogt chrX 100521875 100522311 INT_STITCHED_8704 8132 Cdx4 . Cdx4 chrX 100633203 100633921 INT_STITCHED_8705 545 Tsix . Tsix chrX 101176973 101183244 INT_STITCHED_8708 520 Rlim . Rlim chrX 101391779 101392412 INT_STITCHED_8709 4316 C77370 . C77370 chrX 103119917 103120479 INT_STITCHED_8713 7677 Atrx . Atrx chrX 103207250 103207835 INT_STITCHED_8714 3325 Cox7b, . Magt1 Magt1 chrX 106210257 106210674 INT_STITCHED_8718 6403 Hmgn5 . Hmgn5 chrX 131251894 131252554 INT_STITCHED_8736 2782 Armcx1 . Armcx1 chrX 133571771 133572514 INT_STITCHED_8739 4136 Mcart6 . Mcart6 chrX 136317111 136317651 INT_STITCHED_8742 2358 Ripply1 . Ripply1 chrX 136990746 136995388 INT_STITCHED_8745 2167 Prps1 . Prps1 chrX 146912148 146912772 INT_STITCHED_8754 1199 . Tmem29 Tmem29 chrX 147484225 147485001 INT_STITCHED_8756 2685 Fgd1 . Fgd1 chrX 150159561 150160090 INT_STITCHED_8766 6795 2210013O21Rik . 2210013O21Rik chrX 151776277 151776643 INT_STITCHED_8767 7880 Prdx4 . Prdx4 chrX 153930097 153930709 INT_STITCHED_8769 4541 Sms . Sms chrX 154034237 154039879 INT_STITCHED_8771 1270 Mbtps2 . Mbtps2 chrX 154253329 154253706 INT_STITCHED_8773 7680 Klh134 . Klh134 chrX 159193849 159194432 INT_STITCHED_8781 2630 Rbbp7 . Rbbp7 chrX 159269864 159270795 INT_STITCHED_8782 1741 Txlng . Txlng

TABLE S3A Overlap with previously defined domain structures or interactions Overlap (at Overlap (at Sets of SMC1 least 80% least 80% high-confidence reciprocal) Out of # reciprocal) interactions (X) Testing Query (Y) Metric (counts) interactions (percentage) all SMC1 ChIA-PET Reciprocal 1251 23739  5% intrachromosomal DeMare et al., overlap interactions (limb bud) CTCF-CTCF CTCF ChIA-PET Reciprocal 6770 20080 34% Interactions PETs Handoko et overlap al. SD boundary CTCF ChIA-PET Reciprocal 65 197 33% interactions PETs Handoko et overlap al. SD boundary TD/TAD Dixon et Reciprocal 5 197  3% interactions al. overlap SD boundary TD/TAD Filippova Reciprocal 16 197  8% interactions et al. overlap SD boundary SMC1 ChIA-PET Reciprocal 16 197  8% interactions DeMare et al., overlap (limb bud) PD boundary CTCF ChIA-PET Reciprocal 115 349 33% interactions PETs Handoko et overlap al. PD boundary TD/TAD Dixon et Reciprocal 13 349  4% interactions al. overlap PD boundary TD/TAD Filippova Reciprocal 30 349  9% interactions et al. overlap PD boundary SMC1 ChIA-PET Reciprocal 29 349  8% interactions DeMare et al., overlap (limb bud) Enhancer- PolII ChIA-PET Reciprocal 873 2921 30% Promoter interactions overlap interactions Kieffer-Kwon et al. Enhancer- PolII ChIA-PET Reciprocal 2402 2921 82% Promoter PETs Kieffer-Kwon overlap interactions et al. Enhancer- PolII ChIA-PET Reciprocal 511 2700 19% Enhancer interactions overlap interactions Kieffer-Kwon et al. Enhancer- PolII ChIA-PET Reciprocal 1969 2700 73% Enhancer PETs Kieffer-Kwon overlap interactions et al. Promoter- PolII ChIA-PET Reciprocal 264 818 32% Promoter interactions overlap interactions Kieffer-Kwon et al. Promoter- PolII ChIA-PET Reciprocal 649 818 79% Promoter PETs Kieffer-Kwon overlap interactions et al. Sets of SMC1 Interactions Interactions high-confidence Crossing Out of # Crossing Y interactions (X) Testing Query (Y) Metric Y (counts) interactions (percentage) all TD/TAD % X 1,354 23,739 6% intrachromosomal boundaries Dixon spanning interactions et al. Y all LAD boundaries % X 1,180 23,739 5% intrachromosomal Meuleman et al. spanning interactions Y all LOCK boundaries % X 1,053 23,739 4% intrachromosomal Wen et al. spanning interactions Y

TABLE S3B NPC 5C interactions that are overlapped with SMC1 interactions Thick Thick Item Block Block Block Chr Start End ID Score Strand Start End Rgb Count Sizes Starts chr17 35876754 36004126 chr17: 999 + 35876754 36004126 0, 0, 0 2 1213, 0, 35876754- 7320 120052 36004126 chr16 91081692 91315585 chr16: 999 + 91081692 91315585 0, 0, 0 2 8121, 0, 91081692- 6123 227770 91315585 chr6 122605776 122670401 chr6: 999 + 122605776 122670401 0, 0, 0 2 8322, 0, 122605776- 3902 60723 122670401 chr16 91079632 91353041 chr16: 999 + 91079632 91353041 0, 0, 0 2 2059, 0, 91079632- 2468 270941 91353041 chr17 35309283 35369792 chr17: 999 + 35309283 35369792 0, 0, 0 2 12375, 0, 35309283- 17869 42640 35369792 chr17 35300042 35369792 chr17: 999 + 35300042 35369792 0, 0, 0 2 7232, 0, 35300042- 17869 51881 35369792 chr17 35712435 35863083 chr17 999 + 35712435 35863083 0, 0, 0 2 3047, 0, 35712435- 2345 148303 35863083 chr17 35770148 35873306 chr17: 999 + 35770148 35873306 0, 0, 0 2 3903, 0, 35770148- 9716 93442 35873306 chr16 91079632 91365059 chr16: 999 + 91079632 91365059 0, 0, 0 2 2059, 0, 91079632- 7174 278253 91365059 chr17 35782938 35876753 chr17: 999 + 35782938 35876753 0, 0, 0 2 5265, 0, 35782938- 2748 91067 35876753 chr16 91159407 91315585 chr16: 999 + 91159407 91315585 0, 0, 0 2 2410, 0, 91159407- 6123 150055 91315585

TABLE S4A Super-enhancer Domains Chr Start End chr4 137282987 137358228 chr4 141062149 141133641 chr9 121156481 121284570 chr3 34536922 34661110 chr12 111691772 111830585 chr19 5817540 5852134 chr12 111691772 111729264 chr7 30965803 30984969 chr1 169150382 169237365 chr1 137067918 137266493 chr4 154502843 154625262 chr1 36960319 37190152 chr13 98004422 98291871 chr14 64117842 64155310 chr6 142425554 142468451 chr1 72810841 72902355 chr19 5792497 5886724 chr7 87300923 87362292 chr2 71454171 71655886 chr1 34061676 34222447 chr12 57342031 57506908 chr1 120460689 120657075 chr2 154237288 154366317 chr15 97065222 97329663 chr5 116814343 116927034 chr7 86283831 86495624 chr18 40414663 42171491 chr11 66718693 66799394 chr6 91615554 91692012 chr10 66463947 66597903 chr6 145190466 145291289 chr4 141560318 141655254 chr1 72212313 72267390 chr7 38784232 38860117 chr3 132992046 133215781 chr14 71017056 71047830 chr1 121241277 121341353 chr7 152031593 152075769 chr11 97517094 97528498 chr17 35620607 35672311 chr15 103312356 103379385 chr10 76592621 76716478 chr12 56533123 56600970 chr8 34878299 35059244 chr11 97505763 97552130 chr9 58094359 58130191 chr10 84916886 85088671 chr12 111654141 112084206 chr6 125371654 125449180 chr8 12388966 12513419 chr11 117730560 117880702 chr18 75423941 75656017 chr17 35620607 35647314 chr2 30879347 31008384 chr7 4507929 4892642 chr19 5792497 5852134 chr13 110403658 110714021 chr1 35895775 36192303 chr14 76877794 77141159 chr16 23087368 23136382 chr8 44336405 44414870 chr10 21320132 21716683 chr1 138461016 138635417 chr6 83829249 84014273 chr8 74794083 74890930 chr18 38531148 38620561 chr3 9397733 9706079 chr6 39365369 39397187 chr2 152529858 152569327 chr9 78205346 78234729 chr12 12629041 13017241 chr10 79495253 79527506 chr2 162823799 162916341 chr6 122257932 122343761 chr9 110824885 110900571 chr3 96354611 96386636 chr17 37050504 37341488 chr12 111654141 111913505 chr1 183851391 184046719 chr5 53745413 53986500 chr4 98405832 98554929 chr7 147116120 147156352 chr10 75359462 75415411 chr10 75329011 75415411 chr3 96470813 96497406 chr7 13594061 13617283 chr19 23089343 23229072 chr11 77648017 77759107 chr2 31988954 32048213 chr19 21808238 22379774 chr18 36287108 36489385 chr10 66375750 66564168 chr8 37594982 37753361 chr6 66911889 67093167 chr2 151937066 152023854 chr1 168052731 168085769 chr8 93337017 93461643 chr10 20753144 20909870 chr1 182803710 182905559 chr3 34048462 35382238 chr2 168565336 168670183 chr5 64977526 65258932 chr11 116942064 117039648 chr1 91755202 91840923 chr6 122689212 122737156 chr19 25549889 25621172 chr11 8465819 8761806 chr4 118687950 118815868 chr5 135407901 135444028 chr4 138002737 138021762 chr9 114434686 114494861 chr17 31865371 32163212 chr18 35180089 35693422 chr5 123571740 123606315 chr13 96159680 96721858 chr11 11925186 12441361 chr11 117823113 117880702 chr1 182849231 182905559 chr11 54692478 54798550 chr11 52163912 52188686 chr7 70896448 71205797 chr6 64923531 65029967 chr8 91467275 91572066 chr14 55642580 55796912 chr11 33236011 33455087 chr11 88365951 88591129 chr11 102169637 102201539 chr4 141717621 141806679 chr3 96350545 96443947 chr16 84734897 84880243 chr11 66718693 66899782 chr4 140985352 141133641 chr7 3198402 3222975 chr19 5792497 5878810 chr9 56261740 56401717 chr3 135071737 135395232 chr2 20335900 20595748 chr17 26603012 26776615 chr2 33256274 33352075 chr17 71086210 71216894 chr15 77055148 77199664 chr12 87742959 87956056 chr17 71195618 71250889 chr17 47609255 47735975 chr14 55695067 55717888 chr11 107243228 107335537 chr14 105796075 106303003 chr10 59356750 59468872 chr12 55300475 55591628 chr8 87984083 88051875 chr17 29556459 29652227 chr4 125162485 125485934 chr14 49201179 49509716 chr3 88348083 88408550 chr7 52792902 52845517 chr12 103939956 103958858 chr17 29181193 29233320 chr9 57885470 58130191 chr14 21955683 22561917 chr19 53493838 53654456 chr11 66718693 66839583 chr2 165910064 165985682 chr17 66674595 66840188 chr2 71492827 71652869 chr7 31224743 31258292 chr1 182803710 182832479 chr3 129222980 129325895 chr6 122618790 122670811 chr1 120667669 120981204 chr16 8685741 8795721 chr11 69467645 69529968 chr7 119787192 119837366 chr4 126832402 126893727 chr11 116932982 117039648 chr14 65244350 65372358 chr11 69494914 69529968 chr18 61707865 61826914 chr17 10086176 10938877 chr5 120021125 120139928 chr4 147451592 147468949 chr3 95436247 95482321 chr11 97505763 97601227 chr9 58048791 58130191 chr2 162873366 162916341 chr11 98813654 98828524 chr10 44047591 44482037 chr1 13041583 13125339 chr12 88134365 88316531 chr8 87162269 87234127 chr1 120989689 121341353 chr7 140223741 140326676 chr4 140812787 140920032 chr12 88211553 88248387 chr17 37130666 37222465 chr11 8887662 9037343 chr1 138669873 138901249 chr5 118882848 119045654

TABLE S4B Super-enhancers and their associated Super-enhancer Domains Chr Start End SE Rank in SDs chr7 3193004 3218183 INT_STITCHED_3467 1 TRUE chr3 34633687 34660705 INT_STITCHED_1482 2 TRUE chr12 87839385 87846192 INT_STITCHED_6113 3 TRUE chr9 110849422 110863371 INT_STITCHED_4748 4 TRUE chr8 37602064 37613850 INT_STITCHED_4033 6 TRUE chr4 140826072 140840922 INT_STITCHED_2291 8 TRUE chr3 95455034 95468269 INT_STITCHED_1626 9 TRUE chr2 154242651 154254374 INT_STITCHED_1210 10 TRUE chr17 37110202 37134996 INT_STITCHED_7792 12 TRUE chr6 122290093 122293017 INT_STITCHED_3342 13 TRUE chr9 78207143 78223442 INT_STITCHED_4657 14 TRUE chr8 91514813 91540176 INT_STITCHED_4179 15 TRUE chr19 5835881 5847014 INT_STITCHED_8324 16 TRUE chr17 66818723 66836409 INT_STITCHED_7876 17 TRUE chr2 162877048 162893236 INT_STITCHED_1257 18 TRUE chr9 58119837 58128504 INT_STITCHED_4555 19 TRUE chr6 64961359 64985161 INT_STITCHED_3120 20 TRUE chr7 152036872 152050716 INT_STITCHED_3914 21 TRUE chr12 87807046 87820319 INT_STITCHED_6112 22 TRUE chr4 118743867 118745786 INT_STITCHED_2152 23 TRUE chr11 97517673 97524159 INT_STITCHED_5711 24 TRUE chr2 20574602 20591747 INT_STITCHED_746 25 TRUE chr17 71177302 71179956 INT_STITCHED_7886 26 TRUE chr14 76894682 76915946 INT_STITCHED_6904 27 TRUE chr17 31939569 31956756 INT_STITCHED_7767 29 TRUE chr1 13049615 13094765 INT_STITCHED_45 30 TRUE chr2 32008891 32030736 INT_STITCHED_812 31 TRUE chr6 122640118 122657871 INT_STITCHED_3348 32 TRUE chr3 34544904 34553511 INT_STITCHED_1480 34 TRUE chr5 118884660 118896412 INT_STITCHED_2745 35 TRUE chr8 37642521 37671979 INT_STITCHED_4034 36 TRUE chr12 12790432 12795881 INT_STITCHED_5875 38 TRUE chr4 141120768 141126477 INT_STITCHED_2292 39 TRUE chr6 122714316 122720862 INT_STITCHED_3349 40 TRUE chr5 123584659 123590728 INT_STITCHED_2770 41 TRUE chr17 71213804 71222433 INT_STITCHED_7887 42 TRUE chr19 23139991 23170189 INT_STITCHED_8385 43 TRUE chr3 135208956 135210744 INT_STITCHED_1749 44 TRUE chr12 12933791 12950936 INT_STITCHED_5880 45 TRUE chr17 71096763 71100905 INT_STITCHED_7884 46 TRUE chr11 117833701 117838253 INT_STITCHED_5831 47 TRUE chr11 33427175 33451476 INT_STITCHED_5427 48 TRUE chr1 37039139 37045411 INT_STITCHED_108 49 TRUE chr7 140304156 140307245 INT_STITCHED_3856 51 TRUE chr4 141616653 141627603 INT_STITCHED_2295 52 TRUE chr16 84769173 84780686 INT_STITCHED_7597 53 TRUE chr1 182854521 182864307 INT_STITCHED_611 54 TRUE chr10 79508474 79515168 INT_STITCHED_5111 55 TRUE chr2 33282029 33300860 INT_STITCHED_817 56 TRUE chr11 116943025 116953583 INT_STITCHED_5819 57 TRUE chr11 77697704 77718786 INT_STITCHED_5597 58 TRUE chr1 182818684 182819554 INT_STITCHED_610 59 TRUE chr11 8466451 8486876 INT_STITCHED_5325 61 TRUE chr14 64118817 64131901 INT_STITCHED_6859 62 TRUE chr14 77015215 77030315 INT_STITCHED_6906 63 TRUE chr14 71022659 71035930 INT_STITCHED_6887 66 TRUE chr11 12357626 12370205 INT_STITCHED_5340 67 TRUE chr10 21700576 21708946 INT_STITCHED_4893 68 TRUE chr3 96380383 96382115 INT_STITCHED_1629 69 TRUE chr11 69517060 69522803 INT_STITCHED_5565 70 TRUE chr5 53933177 53947327 INT_STITCHED_2510 71 TRUE chr7 147131117 147136231 INT_STITCHED_3890 72 TRUE chr1 120971968 120973737 INT_STITCHED_372 73 TRUE chr11 66824791 66838230 INT_STITCHED_5555 74 TRUE chr3 133181431 133197648 INT_STITCHED_1744 75 TRUE chr19 25553498 25564092 INT_STITCHED_8399 77 TRUE chr18 61787544 61788400 INT_STITCHED_8209 78 TRUE chr8 87174072 87174643 INT_STITCHED_4163 79 TRUE chr17 37209046 37217726 INT_STITCHED_7794 80 TRUE chr13 96295094 96306119 INT_STITCHED_6544 81 TRUE chr19 23207455 23208806 INT_STITCHED_8386 82 TRUE chr18 40467587 40468140 INT_STITCHED_8148 83 TRUE chr5 65255735 65256794 INT_STITCHED_2535 84 TRUE chr15 77168852 77187251 INT_STITCHED_7248 85 TRUE chr11 88481360 88491812 INT_STITCHED_5666 86 TRUE chr7 31248315 31250619 INT_STITCHED_3525 87 TRUE chr12 55407498 55415046 INT_STITCHED_5995 89 TRUE chr12 88239069 88245155 INT_STITCHED_6118 90 TRUE chr18 75520332 75527277 INT_STITCHED_8261 91 TRUE chr11 9015537 9017663 INT_STITCHED_5331 92 TRUE chr1 137071028 137096284 INT_STITCHED_449 93 TRUE chr6 39395571 39396779 INT_STITCHED_3045 94 TRUE chr2 168589688 168617170 INT_STITCHED_1300 95 TRUE chr1 120538712 120545414 INT_STITCHED_368 96 TRUE chr1 168054897 168073079 INT_STITCHED_556 97 TRUE chr1 72839563 72858199 INT_STITCHED_237 99 TRUE chr4 98507649 98514709 INT_STITCHED_2076 100 TRUE chr16 23099373 23103471 INT_STITCHED_7434 101 TRUE chr7 71092246 71102481 INT_STITCHED_3601 102 TRUE chr19 21858770 21866770 INT_STITCHED_8378 103 TRUE chr2 152002668 152003777 INT_STITCHED_1196 104 TRUE chr4 137329436 137357766 INT_STITCHED_2268 108 TRUE chr5 120029649 120037063 INT_STITCHED_2752 109 TRUE chr14 106296486 106304433 INT_STITCHED_6982 110 TRUE chr4 141721916 141726166 INT_STITCHED_2297 111 TRUE chr3 129247012 129261362 INT_STITCHED_1732 112 TRUE chr9 114458126 114474355 INT_STITCHED_4766 113 TRUE chr17 10549089 10570838 INT_STITCHED_7680 114 TRUE chr2 71488013 71494617 INT_STITCHED_928 115 TRUE chr3 96479158 96484864 INT_STITCHED_1630 116 TRUE chr12 111725920 111743677 INT_STITCHED_6188 117 TRUE chr14 22293688 22308989 INT_STITCHED_6709 118 TRUE chr6 125383335 125398024 INT_STITCHED_3360 119 TRUE chr2 165981373 165983444 INT_STITCHED_1279 121 TRUE chr1 183948212 183961841 INT_STITCHED_615 123 TRUE chr6 91640161 91661247 INT_STITCHED_3217 124 TRUE chr8 12499468 12504771 INT_STITCHED_3947 125 TRUE chr11 102190649 102193692 INT_STITCHED_5741 126 TRUE chr6 67061148 67064202 INT_STITCHED_3130 127 TRUE chr10 85002060 85006553 INT_STITCHED_5140 129 TRUE chr8 87996475 87997654 INT_STITCHED_4167 130 TRUE chr8 93351924 93355292 INT_STITCHED_4190 131 TRUE chr10 75335464 75345568 INT_STITCHED_5091 132 TRUE chr12 111709296 111710794 INT_STITCHED_6187 133 TRUE chr10 66546199 66564235 INT_STITCHED_5059 134 TRUE chr10 21546502 21549691 INT_STITCHED_4891 135 TRUE chr7 38812914 38816123 INT_STITCHED_3550 136 TRUE chr1 121295085 121296031 INT_STITCHED_376 137 TRUE chr7 86355826 86368339 INT_STITCHED_3652 138 TRUE chr17 26631721 26648689 INT_STITCHED_7728 139 TRUE chr14 106250319 106260753 INT_STITCHED_6981 140 TRUE chr17 47640414 47649043 INT_STITCHED_7822 141 TRUE chr5 135417523 135421698 INT_STITCHED_2830 142 TRUE chr4 125211671 125223450 INT_STITCHED_2192 143 TRUE chr11 107296669 107310982 INT_STITCHED_5768 144 TRUE chr14 55704349 55705463 INT_STITCHED_6815 145 TRUE chr2 162856904 162860933 INT_STITCHED_1256 146 TRUE chr8 74834685 74840663 INT_STITCHED_4116 147 TRUE chr15 97198605 97227633 INT_STITCHED_7317 148 TRUE chr18 36412873 36414154 INT_STITCHED_8124 149 TRUE chr9 56382386 56395769 INT_STITCHED_4546 151 TRUE chr1 36111164 36118698 INT_STITCHED_101 152 TRUE chr5 116845764 116860853 INT_STITCHED_2736 153 TRUE chr7 30982397 30983339 INT_STITCHED_3523 154 TRUE chr1 138841643 138850970 INT_STITCHED_466 156 TRUE chr17 29587776 29588942 INT_STITCHED_7752 157 TRUE chr1 138586629 138593131 INT_STITCHED_464 158 TRUE chr19 53523440 53535319 INT_STITCHED_8519 159 TRUE chr8 44405736 44406755 INT_STITCHED_4046 161 TRUE chr7 4772296 4777612 INT_STITCHED_3475 162 TRUE chr6 83839914 83844315 INT_STITCHED_3184 163 TRUE chr10 66380351 66383761 INT_STITCHED_5054 164 TRUE chr12 56587347 56607146 INT_STITCHED_6000 165 TRUE chr7 119831735 119835688 INT_STITCHED_3765 166 TRUE chr18 35202713 35203454 INT_STITCHED_8114 169 TRUE chr1 121201424 121202481 INT_STITCHED_374 170 TRUE chr5 118951444 118960269 INT_STITCHED_2746 171 TRUE chr7 13599334 13600325 INT_STITCHED_3481 172 TRUE chr8 35023426 35027483 INT_STITCHED_4014 173 TRUE chr3 9641461 9655131 INT_STITCHED_1392 174 TRUE chr11 66733372 66746990 INT_STITCHED_5553 177 TRUE chr2 152552277 152563676 INT_STITCHED_1198 178 TRUE chr1 34130107 34134640 INT_STITCHED_88 179 TRUE chr10 59420365 59437537 INT_STITCHED_5021 181 TRUE chr13 98202400 98225162 INT_STITCHED_6559 182 TRUE chr10 75400370 75401358 INT_STITCHED_5092 183 TRUE chr11 54767341 54785832 INT_STITCHED_5499 184 TRUE chr12 12810177 12811020 INT_STITCHED_5876 185 TRUE chr17 35639211 35642435 INT_STITCHED_7784 186 TRUE chr10 76655655 76662360 INT_STITCHED_5100 187 TRUE chr10 44110139 44112766 INT_STITCHED_4981 188 TRUE chr1 72260528 72261272 INT_STITCHED_230 189 TRUE chr1 169201106 169220423 INT_STITCHED_559 190 TRUE chr14 49273113 49283200 INT_STITCHED_6789 191 TRUE chr4 126875757 126879027 INT_STITCHED_2205 192 TRUE chr3 88375442 88380083 INT_STITCHED_1607 193 TRUE chr11 98823511 98826466 INT_STITCHED_5719 194 TRUE chr4 147459254 147463850 INT_STITCHED_2317 196 TRUE chr12 103940487 103953004 INT_STITCHED_6151 197 TRUE chr18 75504155 75505202 INT_STITCHED_8260 198 TRUE chr17 29209618 29218426 INT_STITCHED_7747 200 TRUE chr7 52806853 52814768 INT_STITCHED_3568 201 TRUE chr17 71241991 71250610 INT_STITCHED_7888 203 TRUE chr16 8758173 8779472 INT_STITCHED_7359 204 TRUE chr13 110418702 110442750 INT_STITCHED_6615 206 TRUE chr10 20802131 20830236 INT_STITCHED_4885 207 TRUE chr18 38538325 38551037 INT_STITCHED_8136 208 TRUE chr7 87333420 87345334 INT_STITCHED_3662 209 TRUE chr4 154563584 154564383 INT_STITCHED_2355 210 TRUE chr9 121244501 121254102 INT_STITCHED_4802 213 TRUE chr1 36070190 36074608 INT_STITCHED_100 215 TRUE chr2 30913257 30925299 INT_STITCHED_803 216 TRUE chr13 98052562 98062842 INT_STITCHED_6557 217 TRUE chr11 52173182 52184686 INT_STITCHED_5484 218 TRUE chr14 65251303 65269514 INT_STITCHED_6864 219 TRUE chr4 154537213 154538078 INT_STITCHED_2354 220 TRUE chr12 111655417 111656705 INT_STITCHED_6186 221 TRUE chr6 142458188 142461905 INT_STITCHED_3429 222 TRUE chr2 71575856 71583914 INT_STITCHED_931 223 TRUE chr6 39370384 39371286 INT_STITCHED_3044 225 TRUE chr12 57385208 57400114 INT_STITCHED_6004 226 TRUE chr15 103349226 103353500 INT_STITCHED_7343 227 TRUE chr4 138000554 138006368 INT_STITCHED_2273 228 TRUE chr6 145223385 145225674 INT_STITCHED_3450 230 TRUE chr1 91766947 91773527 INT_STITCHED_315 231 TRUE

TABLE S4C Super-enhancer associated genes in SDs Chr Start End Gene_ID Strand RefSeq_ID Symbol chr1 13103508 13117244 NM_001081209:Prdm14 − NM_001081209 Prdm14 chr1 34068669 34365497 NM_133833:Dst + NM_133833 Dst chr1 34068669 34365497 NM_134448:Dst + NM_134448 Dst chr1 36849033 36996372 NM_018872:Tmem131 − NM_018872 Tmem131 chr1 72205806 72258881 NM_001005423:Mreg − NM_001005423 Mreg chr1 72871076 72899045 NM_008342:Igfbp2 + NM_008342 Igfbp2 chr1 120730637 120950196 NM_001081125:Gli2 − NM_001081125 Gli2 chr1 138740160 138850207 NM_001159769:Nr5a2 − NM_001159769 Nr5a2 chr1 168028278 168058029 NM_001160049:Dusp27 − NM_001160049 Dusp27 chr1 169156216 169215258 NM_030724:Uck2 − NM_030724 Uck2 chr1 183834575 183950111 NM_010135:Enah − NM_010135 Enah chr1 183834575 183950111 NM_001083121:Enah − NM_001083121 Enah chr1 183834575 183950111 NM_001083120:Enah − NM_001083120 Enah chr1 36125244 36163291 NM_015818:Hs6st1 + NM_015818 Hs6st1 chr1 91824536 91827751 NM_010262:Gbx2 − NM_010262 Gbx2 chr1 120524521 120581745 NM_023755:Tcfcp2l1 + NM_023755 Tcfcp2l1 chr1 121312041 121318825 NM_008381:Inhbb − NM_008381 Inhbb chr1 137150150 137155049 NM_007921:Elf3 − NM_007921 Elf3 chr1 138521477 138526968 NM_001160251:Zfp281 + NM_001160251 Zfp281 chr1 138521477 138526968 NM_177643:Zfp281 + NM_177643 Zfp281 chr1 168060590 168096641 NM_021610:Gpa33 + NM_021610 Gpa33 chr1 182823249 182829233 NM_177099:Lefty2 + NM_177099 Lefty2 chr1 182872648 182905235 NM_144794:Tmem63a + NM_144794 Tmem63a chr1 182865169 182868532 NM_010094:Lefty1 + NM_010094 Lefty1 chr2 20431673 20732162 NM_178059:Etl4 + NM_178059 Etl4 chr2 20431673 20732162 NM_029895:Etl4 + NM_029895 Etl4 chr2 30881725 30997528 NM_001177648:Fnbp1 − NM_001177648 Fnbp1 chr2 71557473 71569023 NM_201366:Gm1631 + NM_201366 Gm1631 chr2 154262219 154365092 NM_009823:Cbfa2t2 + NM_009823 Cbfa2t2 chr2 165898588 165981156 NM_028072:Sulf2 − NM_028072 Sulf2 chr2 32006667 32090057 NM_001159634:Bat2l + NM_001159634 Bat2l chr2 33261627 33286844 NM_001085507:Zbtb34 − NM_001085507 Zbtb34 chr2 151969344 151974832 NM_009328:Tcf15 + NM_009328 Tcf15 chr2 152562009 152563146 NM_010495:Id1 + NM_010495 Id1 chr2 162880370 162910423 NM_008652:Mybl2 + NM_008652 Mybl2 chr2 162843207 162871871 NM_172150:Ift52 + NM_172150 Ift52 chr2 168573831 168592701 NM_201395:Sall4 − NM_201395 Sall4 chr2 168573831 168592701 NM_175303:Sall4 − NM_175303 Sall4 chr2 168573831 168592701 NM_201396:Sall4 − NM_201396 Sall4 chr3 9427009 9610085 NM_133218:Zfp704 − NM_133218 Zfp704 chr3 133126640 133207354 NM_001040400:Tet2 − NM_001040400 Tet2 chr3 129235303 129341411 NM_130450:Elovl6 + NM_130450 Elovl6 chr3 34537385 34537464 NR_035433:Mir1897 + NR_035433 Mir1897 chr3 34548926 34551382 NM_011443:Sox2 + NM_011443 Sox2 chr3 88383592 88392335 NM_025448:Ssr2 + NM_025448 Ssr2 chr3 95462642 95467101 NM_008562:Mcl1 + NM_008562 Mcl1 chr3 96361879 96365780 NM_023719:Txnip + NM_023719 Txnip chr3 96400558 96403701 NM_001024851:Ankrd34a + NM_001024851 Ankrd34a chr3 96381796 96398081 NM_027241:Polr3gl − NM_027241 Polr3gl chr3 96474053 96494957 NM_001081139:Ankrd35 + NM_001081139 Ankrd35 chr3 135148574 135234367 NM_027288:Manba + NM_027288 Manba chr4 126846514 126914266 NM_198618:Dlgap3 + NM_198618 Dlgap3 chr4 98421582 98484228 NM_172872:Kank4 − NM_172872 Kank4 chr4 125168074 125391417 NM_001081097:Grik3 + NM_001081097 Grik3 chr4 147451169 147462173 NM_009642:Agtrap − NM_009642 Agtrap chr4 154528183 154596644 NM_011385:Ski − NM_011385 Ski chr4 118781349 118809934 NM_011400:Slc2a1 + NM_011400 Slc2a1 chr4 137297646 137352292 NM_007431:Alpl − NM_007431 Alpl chr4 138011062 138016041 NM_025451:Camk2n1 + NM_025451 Camk2n1 chr4 140857154 140885293 NM_010139:Epha2 + NM_010139 Epha2 chr4 140988817 140992020 NM_001033374:Gm694 − NM_001033374 Gm694 chr4 141102076 141104228 NR_030695:B330016D10Rik + NR_030695 B330016D10Rik chr4 141640212 141644016 NR_027137:Gm10565 + NR_027137 Gm10565 chr4 141695154 141795316 NM_001109685:9030409G11Rik − NM_001109685 9030409G11Rik chr5 53947017 54048684 NM_001080928:Rbpj + NM_001080928 Rbpj chr5 119010727 119215446 NM_172424:Med131 + NM_172424 Med131 chr5 65194761 65221368 NM_008453:Klf3 + NM_008453 Klf3 chr5 116858503 116872873 NM_030704:Hspb8 − NM_030704 Hspb8 chr5 116888730 116915496 NR_015595:2410137F16Rik + NR_015595 2410137F16Rik chr5 120120677 120134610 NM_011535:Tbx3 + NM_011535 Tbx3 chr5 120120677 120134610 NM_198052:Tbx3 + NM_198052 Tbx3 chr5 123568188 123582638 NM_175092:Rhof − NM_175092 Rhof chr5 135420992 135422804 NM_009903:Cldn4 − NM_009903 Cldn4 chr6 83864346 83936865 NM_001166371:Zfml + NM_001166371 Zfml chr6 83864346 83936865 NM_008717:Zfml + NM_008717 Zfml chr6 64992660 65066043 NM_007958:Smarcad1 + NM_007958 Smarcad1 chr6 122677826 122692763 NM_011401:Slc2a3 − NM_011401 Slc2a3 chr6 125410283 125444773 NM_007657:Cd9 − NM_007657 Cd9 chr6 39347819 39370368 NM_018810:Mkrn1 − NM_018810 Mkrn1 chr6 66985089 66987401 NM_007836:Gadd45a − NM_007836 Gadd45a chr6 91634060 91709057 NM_009320:Slc6a6 + NM_009320 Slc6a6 chr6 122267748 122287033 NM_007905:Phc1 − NM_007905 Phc1 chr6 122657585 122663796 NM_028016:Nanog + NM_028016 Nanog chr6 122657800 122663573 NM_001080945:Nanogpd + NM_001080945 Nanogpd chr6 142438768 142456463 NM_008492:Ldhb − NM_008492 Ldhb chr6 145165218 145198751 NM_021284:Kras − NM_021284 Kras chr7 38745010 38804571 NM_011274:C80913 − NM_011274 C80913 chr7 71031236 71083801 NM_021366:Klf13 − NM_021366 Klf13 chr7 119822833 120050319 NM_001166584:Tead1 + NM_001166584 Tead1 chr7 140178693 140315166 NM_009980:Ctbp2 − NM_009980 Ctbp2 chr7 3218784 3221016 NR_028425:LOC100303645 + NR_028425 LOC100303645 chr7 3219482 3219561 NR_030276:Mir291b + NR_030276 Mir291b chr7 3220343 3220423 NR_029643:Mir293 + NR_029643 Mir293 chr7 3218626 3218709 NR_029640:Mir290 + NR_029640 Mir290 chr7 3218919 3219001 NR_029641:Mir291a + NR_029641 Mir291a chr7 3219189 3219271 NR_029642:Mir292 + NR_029642 Mir292 chr7 4759615 4763942 NM_133777:Ube2s − NM_133777 Ube2s chr7 13609500 13616381 NM_011588:Trim28 + NM_011588 Trim28 chr7 30971960 30980067 NM_009795:Capns1 − NM_009795 Capns1 chr7 30969189 30971049 NM_009944:Cox7a1 + NM_009944 Cox7a1 chr7 31220000 31230580 NM_007467:Aplp1 − NM_007467 Aplp1 chr7 31245076 31273628 NM_019459:Nphs1 + NM_019459 Nphs1 chr7 31232784 31242534 NM_172898:Kirrel2 − NM_172898 Kirrel2 chr7 52825732 52845078 NM_009737:Bcat2 + NM_009737 Bcat2 chr7 86418151 86506487 NM_018811:Abhd2 + NM_018811 Abhd2 chr7 87331726 87371410 NM_013659:Sema4b + NM_013659 Sema4b chr7 147129754 147131011 NM_009482:Utf1 + NM_009482 Utf1 chr7 152047290 152051148 NM_010202:Fgf4 + NM_010202 Fgf4 chr8 34893115 35040313 NM_019733:Rbpms − NM_019733 Rbpms chr8 93352733 93578407 NM_177224:Chd9 + NM_177224 Chd9 chr8 12395518 12399555 NM_009233:Sox1 + NM_009233 Sox1 chr8 37630792 37676997 NM_015802:Dlc1 − NM_015802 Dlc1 chr8 44380420 44392363 NM_009556:Zfp42 − NM_009556 Zfp42 chr8 74842960 74845553 NM_008452:Klf2 + NM_008452 Klf2 chr8 87185229 87186751 NM_010499:Ier2 − NM_010499 Ier2 chr8 88016515 88051457 NM_173866:Gpt2 + NM_173866 Gpt2 chr8 91551142 91568061 NM_021390:Sall1 − NM_021390 Sall1 chr9 114420390 114473487 NM_001042503:Trim71 − NM_001042503 Trim71 chr9 120873571 121186290 NM_177589:Ulk4 − NM_177589 Ulk4 chr9 56266652 56344743 NM_025812:Hmg20a + NM_025812 Hmg20a chr9 58050703 58056615 NR_033522:1600029O15Rik + NR_033522 1600029O15Rik chr9 58044103 58052126 NM_001161541:Islr2 − NM_001161541 Islr2 chr9 58064986 58097593 NM_008884:Pm1 − NM_008884 Pm1 chr9 78224709 78226395 NM_026480:Ooep − NM_026480 Ooep chr9 78214860 78216006 NM_025274:Dppa5a − NM_025274 Dppa5a chr9 110854048 110886568 NM_028838:Lrrc2 + NM_028838 Lrrc2 chr9 110842111 110848662 NM_011562:Tdgf1 − NM_011562 Tdgf1 chr10 76514923 76629275 NM_009929:Col18a1 − NM_009929 Col18a1 chr10 44156980 44178493 NM_007548:Prdm1 − NM_007548 Prdm1 chr10 85061155 85123037 NM_001017525:Btbd11 + NM_001017525 Btbd11 chr10 20844735 20880790 NM_010848:Myb − NM_010848 Myb chr10 21698477 21719708 NM_001161847:Sgk1 + NM_001161847 Sgk1 chr10 21712028 21719708 NM_001161849:Sgk1 + NM_001161849 Sgk1 chr10 59412422 59414518 NM_029083:Ddit4 − NM_029083 Ddit4 chr10 66474255 66559605 NM_178606:Reep3 − NM_178606 Reep3 chr10 75385968 75395208 NM_008606:Mmp11 − NM_008606 Mmp11 chr10 75398317 75400479 NM_175329:Chchd10 + NM_175329 Chchd10 chr10 75411056 75412391 NM_009514:Vpreb3 + NM_009514 Vpreb3 chr10 79498697 79502404 NM_025554:Polr2e − NM_025554 Polr2e chr10 79516254 79519184 NM_008162:Gpx4 + NM_008162 Gpx4 chr11 8331654 8564538 NM_001083587:Tns3 − NM_001083587 Tns3 chr11 11830501 11927974 NM_001177629:Grb10 − NM_001177629 Grb10 chr11 33111793 33413746 NM_023146:Ranbp17 − NM_023146 Ranbp17 chr11 66838655 66848292 NM_177392:Tmem220 + NM_177392 Tmem220 chr11 88152883 88579543 NM_054043:Msi2 − NM_054043 Msi2 chr11 98821784 98836256 NM_001176528:Rara + NM_001176528 Rara chr11 107069205 107332034 NM_145823:Pitpnc1 − NM_145823 Pitpnc1 chr11 8893144 8911140 NM_008316:Hus1 − NM_008316 Hus1 chr11 52174616 52202898 NM_011694:Vdac1 + NM_011694 Vdac1 chr11 54716427 54723889 NM_008161:Gpx3 + NM_008161 Gpx3 chr11 66725492 66742202 NM_178656:Pirt + NM_178656 Pirt chr11 66891801 66915793 NM_001099635:Myh3 + NM_001099635 Myh3 chr11 69496078 69499056 NM_001159505:Tnfsf13 − NM_001159505 Tnfsf13 chr11 69486611 69495472 NM_030702:Senp3 − NM_030702 Senp3 chr11 77694116 77707374 NM_008952:Pipox − NM_008952 Pipox chr11 97547265 97549939 NM_001085500:Cisd3 + NM_001085500 Cisd3 chr11 97550136 97560698 NM_001163307:Pcgf2 − NM_001163307 Pcgf2 chr11 97524725 97546772 NM_139311:Mllt6 + NM_139311 Mllt6 chr11 102165873 102180410 NM_011551:Ubtf − NM_011551 Ubtf chr11 116976485 117020582 NM_001166507:Sec14l1 + NM_001166507 Sec14l1 chr11 116976485 116990077 NR_029459:Sec14l1 + NR_029459 Sec14l1 chr11 116976485 117020582 NM_028777:Sec14l1 + NM_028777 Sec14l1 chr11 116938096 116940269 NR_027059:2810008D09Rik + NR_027059 2810008D09Rik chr11 117729262 117734840 NM_027919:Tha1 − NM_027919 Tha1 chr11 117827400 117830680 NM_007707:Socs3 − NM_007707 Socs3 chr12 103806792 103943079 NM_172584:Itpk1 − NM_172584 Itpk1 chr12 87762593 87862578 NM_011934:Esrrb + NM_011934 Esrrb chr12 111723948 111821271 NM_012023:Ppp2r5c + NM_012023 Ppp2r5c chr12 111723948 111821271 NM_001081457:Ppp2r5c + NM_001081457 Ppp2r5c chr12 112046007 112079149 NM_011973:Stk30 − NM_011973 Stk30 chr12 12942898 12948642 NM_008709:Mycn − NM_008709 Mycn chr12 55279967 55304861 NM_028133:Egln3 − NM_028133 Egln3 chr12 56590395 56593634 NM_010907:Nfkbia − NM_010907 Nfkbia chr12 57429293 57446881 NM_145442:Mbip − NM_145442 Mbip chr12 88288292 88306314 NM_173735:2310044G17Rik + NM_173735 2310044G17Rik chr12 88221652 88225764 NM_145836:6430527G18Rik − NM_145836 6430527G18Rik chr12 111839604 111905154 NM_030238:Dync1h1 + NM_030238 Dync1h1 chr13 96281683 96295195 NM_007974:F2rl1 − NM_007974 F2rl1 chr13 98011059 98022995 NM_007930:Enc1 + NM_007930 Enc1 chr13 110694016 110694096 NR_035442:Mir1904 + NR_035442 Mir1904 chr14 22319075 22491355 NM_017479:Myst4 + NM_017479 Myst4 chr14 55680495 55710885 NM_001039198:Zfhx2 − NM_001039198 Zfhx2 chr14 65271367 65425133 NM_001081177:Kif13b + NM_001081177 Kif13b chr14 71036011 71042075 NM_008004:Fgf17 − NM_008004 Fgf17 chr14 49277858 49282547 NM_144841:Otx2 − NM_144841 Otx2 chr14 49288962 49413023 NR_029384:Otx2os1 + NR_029384 Otx2os1 chr14 55725662 55735115 NM_177049:Jph4 − NM_177049 Jph4 chr14 55713620 55717832 NM_153083:Thtpa + NM_153083 Thtpa chr14 64111183 64127929 NM_021480:Tdh − NM_021480 Tdh chr14 76904316 76907573 NM_009366:Tsc22d1 + NM_009366 Tsc22d1 chr14 106291163 106296036 NM_011897:Spry2 − NM_011897 Spry2 chr15 76909419 77137483 NM_001110827:Rbm9 − NM_001110827 Rbm9 chr15 76909419 77137483 NM_053104:Rbm9 − NM_053104 Rbm9 chr15 76909419 77137483 NM_175387:Rbm9 − NM_175387 Rbm9 chr15 97074504 97077718 NM_178114:Amigo2 − NM_178114 Amigo2 chr15 97074504 97077718 NM_001164602:Amigo2 − NM_001164602 Amigo2 chr15 97074504 97077718 NM_001164563:Amigo2 − NM_001164563 Amigo2 chr15 103360709 103368423 NM_021391:Ppp1r1a − NM_021391 Ppp1r1a chr16 84774367 84823129 NM_023844:Jam2 + NM_023844 Jam2 chr16 8688814 8738435 NM_001003918:Usp7 − NM_001003918 Usp7 chr16 23107551 23114205 NM_013506:Eif4a2 + NM_013506 Eif4a2 chr16 23107551 23114205 NM_001123038:Eif4a2 + NM_001123038 Eif4a2 chr16 23107551 23114205 NM_001123037:Eif4a2 + NM_001123037 Eif4a2 chr16 23109025 23109093 NR_030705:Snord2 + NR_030705 Snord2 chr17 10399335 10512226 NM_001159517:Qk − NM_001159517 Qk chr17 10403044 10512226 NM_021881:Qk − NM_021881 Qk chr17 10403044 10512226 NM_001159516:Qk − NM_001159516 Qk chr17 35649679 35653769 NM_001163764:Tcf19 − NM_001163764 Tcf19 chr17 35649679 35653769 NM_025674:Tcf19 − NM_025674 Tcf19 chr17 35649679 35653769 NM_001163763:Tcf19 − NM_001163763 Tcf19 chr17 29227930 29237667 NM_001111099:Cdkn1a + NM_001111099 Cdkn1a chr17 31981194 31992737 NM_010831:Sik1 − NM_010831 Sik1 chr17 37091302 37095373 NM_023162:Znrd1 − NM_023162 Znrd1 chr17 66686321 66799090 NM_172963:1110012J17Rik − NM_172963 1110012J17Rik chr17 66686321 66799090 NM_001114098:1110012J17Rik − NM_001114098 1110012J17Rik chr17 26642535 26645417 NM_013642:Dusp1 − NM_013642 Dusp1 chr17 29627989 29632404 NM_008842:Pim1 + NM_008842 Pim1 chr17 35642983 35647722 NM_013633:Pou5f1 + NM_013633 Pou5f1 chr17 35654060 35667960 NM_146248:Cchcr1 + NM_146248 Cchcr1 chr17 37114645 37118182 NM_029747:2410137M14Rik − NM_029747 2410137M14Rik chr17 37138107 37147674 NM_001168502:Zfp57 + NM_001168502 Zfp57 chr17 37095536 37102568 NM_029602:Znrd1as + NM_029602 Znrd1as chr17 37182910 37211250 NM_019439:Gabbr1 + NM_019439 Gabbr1 chr17 37123799 37126449 NM_001115075:H2-M5 − NM_001115075 H2-M5 chr17 37222135 37223181 NM_146477:Olfr90 − NM_146477 Olfr90 chr17 47624998 47639236 NM_022015:Taf8 − NM_022015 Taf8 chr17 47730415 47736637 NM_007632:Ccnd3 + NM_007632 Ccnd3 chr17 71193544 71201074 NM_001164075:Tgif1 − NM_001164075 Tgif1 chr17 71193544 71196117 NM_001164077:Tgif1 − NM_001164077 Tgif1 chr18 35278565 35414429 NM_009818:Ctnna1 + NM_009818 Ctnna1 chr18 36177311 36356814 NM_001167891:Nrg2 − NM_001167891 Nrg2 chr18 40418014 40690838 NM_026135:Kctd16 + NM_026135 Kctd16 chr18 38578628 38624060 NM_022996:Ndfip1 + NM_022996 Ndfip1 chr18 61807478 61807548 NR_029557:Mir145 − NR_029557 Mir145 chr18 75527018 75555588 NM_001042660:Smad7 + NM_001042660 Smad7 chr19 21852831 21932817 NM_001033759:Tmem2 + NM_001033759 Tmem2 chr19 21852831 21932817 NM_031997:Tmem2 + NM_031997 Tmem2 chr19 5878465 5885768 NM_134154:Slc25a45 + NM_134154 Slc25a45 chr19 5850973 5875208 NM_026169:Frmd8 − NM_026169 Frmd8 chr19 5795689 5802671 NR_002847:Malat1 − NR_002847 Malat1 chr19 5842301 5845478 NR_003513:Neat1 − NR_003513 Neat1 chr19 23215715 23241401 NM_010638:Klf9 + NM_010638 Klf9 chr19 23223920 23224041 NR_035423:Mir1192 + NR_035423 Mir1192 chr19 25580195 25678818 NM_015826:Dmrt1 + NM_015826 Dmrt1 chr19 53515701 53539286 NR_028427:5830416P10Rik − NR_028427 5830416P10Rik

TABLE S5A Polycomb Domains Chr Start End chr15 78453437 78575580 chr10 61589218 61647017 chr8 80799571 80992709 chr1 39066910 39268483 chr3 87994703 88039854 chr13 99120951 99232262 chr9 111191818 111217605 chr3 38782628 39605373 chr15 74344113 74369524 chr14 69762825 69854746 chr18 42502366 42628138 chr1 74941139 74963127 chr12 56618442 56822149 chr18 67288025 67431503 chr6 83645094 83677967 chr2 146783872 147005727 chr2 37780790 38232361 chr4 140760096 140824721 chr4 139345249 139415427 chr19 25653445 25698186 chr11 23948726 23983139 chr3 87572271 87621437 chr11 33076054 33455087 chr2 74552598 74804510 chr13 40712815 40845489 chr10 86588382 86967665 chr18 22832286 23286887 chr12 112666820 112698672 chr14 30949584 31274059 chr5 120264806 120539422 chr15 75557525 75579942 chr9 40644350 40791552 chr5 98595699 98759186 chr7 139767015 139850634 chr7 53647930 53863753 chr15 11682493 11840486 chr15 31244932 31349476 chr7 149795933 149858881 chr19 59184016 59271634 chr18 81176251 81423397 chr5 148036975 148106542 chr4 139735055 139809270 chr15 99389024 99428304 chr8 123636646 123738210 chr3 105253211 105478450 chr5 120730927 120891521 chr1 77974835 78416978 chr11 103500171 103620942 chr11 94977809 95022857 chr1 74834000 74856527 chr8 123493766 123617406 chr1 157421785 157632809 chr13 31299149 31713020 chr11 107490351 107715175 chr10 79802236 79813916 chr3 93210295 93298739 chr4 114589269 114620822 chr2 147002703 147083205 chr11 96059282 96208742 chr18 74590407 74732341 chr2 181393443 181414355 chr3 87790216 87876709 chr16 94075259 94481179 chr8 47326713 47392786 chr4 114710430 114758788 chr11 85677002 85786772 chr15 72346773 72854302 chr6 126103930 126118687 chr1 186315551 186562611 chr5 140313918 140402553 chr2 105362765 105522705 chr2 143662464 144279180 chr1 121241277 121341353 chr11 98125902 98204996 chr6 115850549 115958682 chr11 116087328 116156661 chr8 127140592 127352171 chr2 107808286 109535988 chr13 73388336 73448824 chr5 38207655 38343863 chr1 129396087 129577246 chr6 82946180 83216057 chr6 85129186 85190029 chr1 19195103 20504651 chr18 37248918 37379159 chr11 120376481 120474857 chr2 118463167 118522728 chr11 101780380 101831001 chr11 96006370 96085858 chr4 153981410 154050097 chr9 57899009 58053538 chr17 8580889 8655235 chr2 133375372 133856190 chr7 148091905 148125698 chr7 56870962 57009360 chr3 82680738 82800141 chr2 103973933 104263430 chr2 73004649 73120657 chr4 136484379 136527669 chr10 66780210 67192868 chr5 148527856 148628871 chr3 106896401 106991995 chr9 74377669 74719719 chr14 63825457 63977777 chr2 127187661 127261670 chr19 45655337 45822802 chr9 78635225 79569738 chr7 26410442 26486618 chr3 17949132 18059258 chr19 46209175 46329575 chr11 71865741 71959460 chr1 74930650 74940957 chr3 55323975 55805071 chr3 66214095 67149358 chr1 122490637 123077811 chr2 90706201 90902061 chr2 61505881 62124926 chr17 93557330 93932696 chr8 87282578 87337839 chr13 22065408 22121612 chr8 124241314 124276189 chr11 95751315 95802340 chr5 37553758 37681406 chr3 86131864 86566496 chr10 126761070 126780074 chr12 57781525 58087936 chr4 136719874 136844703 chr14 67009269 67404617 chr2 147672633 147936683 chr12 105696987 105785432 chr1 72911922 72926795 chr5 147976190 148040071 chr6 52255415 52528135 chr11 96143184 96166703 chr11 120519625 120541935 chr1 18349577 19169874 chr3 118128160 118695479 chr11 69576597 69620280 chr9 49094744 49295473 chr5 35704009 35818634 chr4 88790816 88957518 chr16 17743009 17813058 chr7 89104078 89265473 chr14 33122592 33287052 chr6 53744181 53909484 chr12 57342031 57642931 chr4 46701340 47034439 chr13 31892385 32049355 chr15 99425402 99509823 chr2 35864545 35998232 chr2 93317161 93499982 chr12 10810937 11186443 chr10 61379340 61444236 chr14 67830035 67869190 chr5 37251936 37312176 chr16 35539620 35597647 chr9 20956721 20974128 chr4 12167572 14363530 chr7 31781201 31863978 chr7 147154506 147249861 chr2 170301302 170335132 chr1 140731509 141053781 chr6 22071418 22397674 chr18 80802693 80926892 chr14 13151609 13364431 chr7 137916138 138126964 chr7 107136814 107178717 chr11 116361766 116396593 chr6 5955031 6835966 chr15 98409888 98630657 chr13 113775570 113827017 chr14 70948562 71038375 chr6 8885196 9185688 chr8 87460671 87471691 chr6 49468491 49870322 chr1 88994744 89073481 chr9 31366495 31734459 chr9 99746742 100202840 chr10 79908131 79970767 chr11 85519669 85659081 chr13 56321977 56362699 chr16 11980485 12202145 chr4 97417187 97911485 chr10 29252035 29524795 chr15 73663090 74369524 chr11 103992553 104033788 chr18 66093628 66125656 chr8 125633945 125715446 chr4 138477307 138635320 chr2 147146382 147205592 chr3 90215853 90271243 chr16 18470420 18618580 chr10 126612870 126621738 chr14 57711442 57982545 chr5 118451662 118520213 chr8 73964776 74234839 chr4 151587708 151753870 chr11 57637946 57732427 chr9 121385947 121581248 chr4 142913865 142971364 chr9 119466739 119490709 chr15 10850327 10969260 chr1 74972911 75064325 chr15 64748903 65157656 chr2 70116066 70402381 chr2 118525313 118586356 chr5 121129209 121165287 chr2 119125322 119338875 chr4 137937707 137983525 chr17 46402394 46436363 chr15 99044494 99097095 chr5 148036975 148132108 chr5 28777131 28797336 chr17 14369226 14426045 chr9 95440367 95574006 chr2 84710105 84730933 chr2 19352305 19442249 chr13 113783396 113827017 chr18 66392485 66564986 chr2 121895058 122129431 chr9 101083779 102257926 chr16 17910946 17939895 chr19 16876605 17060283 chr9 37236402 37271442 chr2 24264226 24425121 chr3 153980376 154236535 chr2 26037592 26084274 chr9 87602547 87636359 chr16 20508899 20643120 chr2 93710179 93843387 chr11 103624481 103773502 chr19 43645038 43699410 chr12 9576159 10445632 chr15 100442477 100469933 chr8 72938972 73031283 chr6 88138316 88193555 chr9 32212249 32398591 chr15 75378540 75491511 chr10 19016883 19212199 chr7 132926269 133234081 chr17 46594272 46648931 chr5 126008996 126060338 chr3 99037342 99092954 chr8 11468672 11486938 chr13 13608409 13960951 chr2 28610521 28833163 chr4 114319862 114620822 chr10 79812609 79837658 chr10 22500836 22801962 chr12 58926308 60049180 chr4 21524834 21624000 chr1 122234083 122366310 chr7 151983330 152038090 chr13 48750476 48775414 chr6 52206381 52789571 chr10 42027361 42322178 chr4 124660720 124737193 chr11 115130964 115216487 chr12 87742959 87956056 chr1 56809694 57035831 chr6 29466717 29600672 chr9 89721374 89869235 chr2 180479038 180515035 chr11 95258699 95383898 chr9 118300480 118399774 chr8 17166802 17538331 chr5 67438839 67493882 chr7 150280034 150325582 chr16 35109416 35273269 chr5 67971103 68119849 chr2 71289578 71386963 chr4 125954539 125987917 chr11 118942545 118953732 chr2 38546606 38595794 chr1 5904967 6125995 chr17 26939804 27024045 chr1 74927030 74940957 chr2 21839013 22578236 chr5 35519528 35692272 chr5 75356242 75540215 chr12 8065982 8314120 chr12 85886346 85931538 chr12 103291998 103420889 chr4 126344059 126419635 chr7 57041827 57179746 chr18 82202955 82739205 chr8 86533322 86546421 chr17 88171992 88278103 chr11 76810383 76907780 chr1 74809202 74831880 chr19 45294566 45319625 chr7 105891216 105990913 chr2 31679069 31704211 chr4 115574868 115626304 chr2 158375206 158455993 chr8 107787790 107808029 chr19 45190897 45236347 chr10 19427631 19614663 chr17 85588047 86033886 chr19 43101550 43471702 chr16 44299003 44363083 chr6 23707772 23837273 chr14 58652944 59130521 chr17 80098100 80241035 chr17 23796716 23884186 chr11 59051979 59107993 chr19 5528726 5569646 chr18 53580157 53832492 chr5 75514435 75553930 chr6 117116125 117127164 chr2 31347377 31511670 chr11 100927557 101039225 chr14 65175865 65243974 chr14 70473679 70497000 chr13 95329322 95712368 chr13 51512928 51714192 chr7 138682999 138739170 chr17 57386369 57417093 chr4 125162485 125173714 chr15 85353258 85414686 chr18 76537526 77130094 chr19 44814055 44963095 chr13 116020184 117504475 chr2 91760879 91774433 chr3 104591025 104771906 chr5 113002319 113073418 chr17 56641571 56688134 chr17 86063603 86463636 chr10 126947405 126975889 chr17 8832553 9001147 chr1 89142254 89190277 chr1 13041583 13125339 chr12 73948167 74064551 chr11 75594932 75717981 chr15 98721260 98736004 chr3 107158587 107266031 chr4 128907441 128950835 chr15 98409888 98488576 chr1 133103585 133143809 chr6 126513425 126653016 chr6 23129575 23413638 chr8 72397734 72415735 chr19 54118289 54324013 chr6 112356746 112651673 chr9 30747116 30890857 chr4 109249104 109693768 chr3 104582317 104592928 chr8 12191468 12565334 chr6 145778132 145918769

TABLE S5B Polycomb target genes in PDs Chr Start End Gene_ID Strand RefSeq_ID Symbol chr1 13103508 13117244 NM_001081209:Prdm14 − NM_001081209 Prdm14 chr1 19093102 19156413 NM_153154:Tcfap2d + NM_153154 Tcfap2d chr1 39251116 39420085 NM_008719:Npas2 + NM_008719 Npas2 chr1 56850824 57028178 NM_139146:Satb2 − NM_139146 Satb2 chr1 74838592 74850749 NM_009518:Wnt10a + NM_009518 Wnt10a chr1 78097841 78193711 NM_008781:Pax3 − NM_008781 Pax3 chr1 78097841 78193711 NM_001159520:Pax3 − NM_001159520 Pax3 chr1 129386918 129574598 NM_028135:Tmem163 − NM_028135 Tmem163 chr1 5903787 5907479 NM_010342:Npbwr1 − NM_010342 Npbwr1 chr1 19198994 19228815 NM_009334:Tcfap2b + NM_009334 Tcfap2b chr1 19202134 19228815 NM_001025305:Tcfap2b + NM_001025305 Tcfap2b chr1 57028312 57032040 NR_024326:9130024F11Rik + NR_024326 9130024F11Rik chr1 57028312 57032040 NR_024325:9130024F11Rik + NR_024325 9130024F11Rik chr1 72904638 72921439 NM_010518:Igfbp5 − NM_010518 Igfbp5 chr1 74818465 74831893 NM_009526:Wnt6 + NM_009526 Wnt6 chr1 74928082 74931982 NM_153111:Fev − NM_153111 Fev chr1 74947231 74947295 NR_029876:Mir375 − NR_029876 Mir375 chr1 74936517 74939709 NM_021541:Cryba2 − NM_021541 Cryba2 chr1 74991891 74998225 NM_010544:Ihh − NM_010544 Ihh chr1 89044229 89051602 NM_021306:Ecel1 − NM_021306 Ecel1 chr1 89160938 89207366 NM_028889:Efhd1 + NM_028889 Efhd1 chr1 121312041 121318825 NM_008381:Inhbb − NM_008381 Inhbb chr1 122237158 122239751 NM_207233:C1ql2 + NM_207233 C1ql2 chr1 122499063 122504568 NM_010133:En1 + NM_010133 En1 chr1 133072986 133141755 NM_018750:Rassf5 − NM_018750 Rassf5 chr1 140721762 140744156 NM_010714:Lhx9 − NM_010714 Lhx9 chr1 140727523 140739021 NM_001042577:Lhx9 − NM_001042577 Lhx9 chr1 140721762 140739021 NM_001025565:Lhx9 − NM_001025565 Lhx9 chr1 157548823 157589157 NM_010712:Lhx4 − NM_010712 Lhx4 chr1 186551023 186556372 NM_008250:Hlx − NM_008250 Hlx chr2 22477846 22549397 NM_008078:Gad2 + NM_008078 Gad2 chr2 103983231 104250491 NM_001033347:D430041D05Rik − NM_001033347 D430041D05Rik chr2 105376236 105510487 NR_002867:Pax6os1 − NR_002867 Pax6os1 chr2 147009818 147157417 NR_030769:Nkx2-2as + NR_030769 Nkx2-2as chr2 147190729 147200784 NM_008780:Pax1 + NM_008780 Pax1 chr2 19367289 19369128 NM_018809:Ptf1a + NM_018809 Ptf1a chr2 24276079 24331086 NM_011040:Pax8 − NM_011040 Pax8 chr2 26055731 26062076 NM_001039653:Lhx3 − NM_001039653 Lhx3 chr2 28763199 28771960 NM_001164186:Barhl1 − NM_001164186 Barhl1 chr2 28763199 28771941 NM_019446:Barhl1 − NM_019446 Barhl1 chr2 31495556 31511315 NM_001123362:Prdm12 + NM_001123362 Prdm12 chr2 31668809 31701525 NM_178887:Fibcd1 − NM_178887 Fibcd1 chr2 35937472 35959580 NM_001083127:Lhx6 − NM_001083127 Lhx6 chr2 35937472 35959580 NM_001083126:Lhx6 − NM_001083126 Lhx6 chr2 35937472 35960928 NM_008500:Lhx6 − NM_008500 Lhx6 chr2 35937472 35960928 NM_001083125:Lhx6 − NM_001083125 Lhx6 chr2 38206827 38225248 NM_010710:Lhx2 + NM_010710 Lhx2 chr2 38548179 38570062 NM_139051:Nr5a1 − NM_139051 Nr5a1 chr2 61642509 61652170 NM_009322:Tbr1 + NM_009322 Tbr1 chr2 70312979 70315783 NM_022435:Sp5 + NM_022435 Sp5 chr2 71368694 71375948 NR_002854:Dlx1as − NR_002854 Dlx1as chr2 71381464 71384811 NM_010054:Dlx2 − NM_010054 Dlx2 chr2 73109982 73113828 NM_001005343:Sp9 + NM_001005343 Sp9 chr2 74601036 74603199 NM_010467:Hoxd1 + NM_010467 Hoxd1 chr2 84712102 84726849 NM_199223:Rtn4rl2 − NM_199223 Rtn4r12 chr2 90725942 90730683 NM_026161:C1qtnf4 + NM_026161 C1qtnf4 chr2 91762345 91769986 NM_007699:Chrm4 + NM_007699 Chrm4 chr2 93482590 93521496 NM_007442:Alx4 + NM_007442 Alx4 chr2 93795966 93797257 NM_001145034:Gm13889 − NM_001145034 Gm13889 chr2 109514856 109567200 NM_007540:Bdnf + NM_007540 Bdnf chr2 118502981 118523756 NM_001145854:Pak6 + NM_001145854 Pak6 chr2 118524838 118529699 NM_001081971:Gm1337 − NM_001081971 Gm1337 chr2 119151519 119161402 NM_019454:Dll4 + NM_019454 Dll4 chr2 119146934 119151933 NR_030683:Gm14207 − NR_030683 Gm14207 chr2 122124635 122128621 NM_025777:Duoxa2 + NM_025777 Duoxa2 chr2 122106172 122123901 NM_177610:Duox2 − NM_177610 Duox2 chr2 127189021 127192957 NM_009633:Adra2b + NM_009633 Adra2b chr2 133378934 133388621 NM_007553:Bmp2 + NM_007553 Bmp2 chr2 144130911 144157816 NM_026924:Ovol2 − NM_026924 Ovol2 chr2 144130911 144157098 NM_152947:Ovol2 − NM_152947 Ovol2 chr2 146909611 146911081 NM_023504:Nkx2-4 − NM_023504 Nkx2-4 chr2 147008887 147012138 NM_010919:Nkx2-2 − NM_010919 Nkx2-2 chr2 147003281 147012138 NM_001077632:Nkx2-2 − NM_001077632 Nkx2-2 chr2 147868613 147872705 NM_010446:Foxa2 − NM_010446 Foxa2 chr2 158436493 158441483 NM_009508:Slc32a1 + NM_009508 Slc32a1 chr2 170308464 170322638 NM_009996:Cyp24a1 − NM_009996 Cyp24a1 chr2 170321927 170344567 NM_001013369:Pfdn4 + NM_001013369 Pfdn4 chr2 180509085 180511605 NM_080641:Bhlhe23 − NM_080641 Bhlhe23 chr2 181404541 181406345 NM_009236:Sox18 − NM_009236 Sox18 chr3 38785861 38910905 NM_183221:Fat4 + NM_183221 Fat4 chr3 17954324 17957514 NM_021560:Bhlhe22 + NM_021560 Bhlhe22 chr3 82696503 82707896 NM_023624:Lrat − NM_023624 Lrat chr3 99057682 99158183 NM_009323:Tbx15 + NM_009323 Tbx15 chr3 105255247 105476920 NM_001039347:Kcnd3 + NM_001039347 Kcnd3 chr3 55586431 55589209 NM_010750:Mab21l1 + NM_010750 Mab21l1 chr3 66777190 66785693 NM_013665:Shox2 − NM_013665 Shox2 chr3 86349502 86352205 NM_011839:Mab21l2 − NM_011839 Mab21l2 chr3 87600872 87620023 NM_011832:Insrr + NM_011832 Insrr chr3 87582165 87599084 NM_001033124:Ntrk1 − NM_001033124 Ntrk1 chr3 87796435 87804278 NM_001109758:Bcan − NM_001109758 Bcan chr3 87791452 87804278 NM_007529:Bcan − NM_007529 Bcan chr3 88019519 88019608 NR_029817:Mir9-1 + NR_029817 Mir9-1 chr3 90254513 90269788 NM_008727:Npr1 − NM_008727 Npr1 chr3 93246251 93252999 NM_001163098:Tchh + NM_001163098 Tchh chr3 104570323 104580465 NM_183224:Fam19a3 − NM_183224 Fam19a3 chr3 104747722 104764627 NM_009520:Wnt2b − NM_009520 Wnt2b chr3 106904484 106909797 NM_008417:Kcna2 + NM_008417 Kcna2 chr3 107241220 107261816 NM_145922:Kcnc4 − NM_145922 Kcnc4 chr3 118136774 118136847 NR_029551:Mir137 + NR_029551 Mir137 chr3 153969257 153993524 NM_010713:Lhx8 − NM_010713 Lhx8 chr4 97444316 97785567 NM_010905:Nfia + NM_010905 Nfia chr4 97444316 97785567 NM_001122953:Nfia + NM_001122953 Nfia chr4 13670448 13820790 NM_001111026:Runx1t1 + NM_001111026 Runx1t1 chr4 46676769 47004586 NM_001081141:Gabbr2 − NM_001081141 Gabbr2 chr4 115587723 115612531 NM_130865:Dmbx1 − NM_130865 Dmbx1 chr4 115587723 115612531 NM_001025567:Dmbx1 − NM_001025567 Dmbx1 chr4 125168074 125391417 NM_001081097:Grik3 + NM_001081097 Grik3 chr4 136833549 136852694 NM_009523:Wnt4 + NM_009523 Wnt4 chr4 139293995 139388883 NM_011039:Pax7 − NM_011039 Pax7 chr4 139582766 139802726 NM_198610:Igsf21 − NM_198610 Igsf21 chr4 153690233 154010982 NM_027504:Prdm16 − NM_027504 Prdm16 chr4 153690233 154010982 NM_001177995:Prdm16 − NM_001177995 Prdm16 chr4 21604626 21613110 NM_001080771:Prdm13 − NM_001080771 Prdm13 chr4 88920376 88928096 NM_001040654:Cdkn2a − NM_001040654 Cdkn2a chr4 109650629 109656289 NM_172296:Dmrta2 + NM_172296 Dmrta2 chr4 114597751 114598618 NM_015758:Foxe3 − NM_015758 Foxe3 chr4 114578884 114581503 NM_008593:Foxd2 − NM_008593 Foxd2 chr4 114581893 114593723 NR_030721:9130206I24Rik + NR_030721 9130206I24Rik chr4 114732131 114744360 NM_011527:Tal1 + NM_011527 Tal1 chr4 124663673 124686343 NM_138683:Rspo1 + NM_138683 Rspo1 chr4 125964037 125991574 NM_199473:Col8a2 + NM_199473 Col8a2 chr4 126393246 126413513 NM_198960:Tcfap2e − NM_198960 Tcfap2e chr4 128896821 128925687 NM_001033189:C77080 − NM_001033189 C77080 chr4 136485333 136512731 NM_007939:Epha8 − NM_007939 Epha8 chr4 137950006 137952373 NM_001081672:Fam43b − NM_001081672 Fam43b chr4 138617323 138630704 NM_021358:Htr6 − NM_021358 Htr6 chr4 140798798 140813477 NM_172520:Arhgef19 + NM_172520 Arhgef19 chr4 142939652 142960931 NM_001162983:Lrrc38 + NM_001162983 Lrrc38 chr4 151660080 151665771 NM_008237:Hes3 − NM_008237 Hes3 chr4 151681131 151692734 NM_001033489:Rnf207 − NM_001033489 Rnf207 chr5 118477832 118511879 NM_021344:Tesc + NM_021344 Tesc chr5 28793523 29045749 NR_015562:9530036O11Rik + NR_015562 9530036O11Rik chr5 98683202 98706049 NM_010203:Fgf5 + NM_010203 Fgf5 chr5 112848177 113006205 NM_019982:Sez6l − NM_019982 Sez6l chr5 120284671 120335227 NM_011537:Tbx5 + NM_011537 Tbx5 chr5 126012787 126272953 NM_001190352:Tmem132b + NM_001190352 Tmem132b chr5 148373771 148537564 NM_010228:Flt1 − NM_010228 Flt1 chr5 28783379 28793641 NM_009170:Shh − NM_009170 Shh chr5 35621214 35624412 NM_007418:Adra2c + NM_007418 Adra2c chr5 35731765 35735521 NM_010445:Hmx1 + NM_010445 Hmx1 chr5 37259808 37346317 NM_172994:Ppp2r2c + NM_172994 Ppp2r2c chr5 37633318 37683370 NM_001136058:Crmp1 + NM_001136058 Crmp1 chr5 38211802 38213990 NR_027920:Msx1as + NR_027920 Msx1as chr5 67485635 67490365 NM_008888:Phox2b − NM_008888 Phox2b chr5 67999121 68003511 NM_001033415:Shisa3 + NM_001033415 Shisa3 chr5 75471625 75473918 NM_133256:Gsx2 + NM_133256 Gsx2 chr5 75548315 75594229 NM_011058:Pdgfra + NM_011058 Pdgfra chr5 75552190 75594229 NM_001083316:Pdgfra + NM_001083316 Pdgfra chr5 98609887 98616467 NM_029947:Prdm8 + NM_029947 Prdm8 chr5 120881894 120891466 NM_008499:Lhx5 + NM_008499 Lhx5 chr5 121130272 121161678 NM_008052:Dtx1 − NM_008052 Dtx1 chr5 140383896 140450678 NM_175522:Elfn1 + NM_175522 Elfn1 chr5 148000271 148002522 NM_008178:Gsx1 + NM_008178 Gsx1 chr5 148081706 148086725 NM_008814:Pdx1 + NM_008814 Pdx1 chr5 148112475 148118825 NM_007673:Cdx2 − NM_007673 Cdx2 chr6 6813333 6817970 NM_010057:Dlx6 + NM_010057 Dlx6 chr6 6770545 6819533 NR_015388:Dlx6os1 − NR_015388 Dlx6os1 chr6 8900018 9198578 NM_008751:Nxph1 + NM_008751 Nxph1 chr6 23212837 23789300 NM_153163:Cadps2 − NM_153163 Cadps2 chr6 126051429 126116762 NM_001164034:Ntf3 − NM_001164034 Ntf3 chr6 126051429 126116762 NM_008742:Ntf3 − NM_008742 Ntf3 chr6 126051429 126114978 NM_001164035:Ntf3 − NM_001164035 Ntf3 chr6 6813796 6815150 NR_002839:Dlx6as − NR_002839 Dlx6as chr6 6827804 6832068 NM_198854:Dlx5 − NM_198854 Dlx5 chr6 6827804 6832068 NM_010056:Dlx5 − NM_010056 Dlx5 chr6 22238226 22248522 NM_053116:Wnt16 + NM_053116 Wnt16 chr6 23195046 23198264 NM_028462:Fezf1 − NM_028462 Fezf1 chr6 29476732 29487319 NM_012057:Irf5 + NM_012057 Irf5 chr6 49772727 49779504 NM_023456:Npy + NM_023456 Npy chr6 52263491 52268372 NM_007966:Evx1 + NM_007966 Evx1 chr6 52208851 52210874 NM_008264:Hoxa13 − NM_008264 Hoxa13 chr6 53765461 53770819 NM_025817:1200009O22Rik − NM_025817 1200009O22Rik chr6 83018318 83020219 NM_009392:Tlx2 − NM_009392 Tlx2 chr6 83661257 83688298 NM_011912:Vax2 + NM_011912 Vax2 chr6 83642799 83662195 NR_002871:Vax2os2 − NR_002871 Vax2os2 chr6 83652095 83660926 NR_002873:Vax2os1 − NR_002873 Vax2os1 chr6 85137924 85154457 NM_010131:Emx1 + NM_010131 Emx1 chr6 88148657 88157026 NM_008090:Gata2 + NM_008090 Gata2 chr6 112423677 112439802 NM_001081147:Oxtr − NM_001081147 Oxtr chr6 115904828 115945023 NM_026376:Plxnd1 − NM_026376 Plxnd1 chr6 117118552 117131386 NM_013655:Cxcl12 + NM_013655 Cxcl12 chr6 117118552 117125087 NM_021704:Cxcl12 + NM_021704 Cxcl12 chr6 117118552 117131386 NM_001012477:Cxcl12 + NM_001012477 Cxcl12 chr6 126586480 126595819 NM_010595:Kcna1 − NM_010595 Kcna1 chr6 145811256 145813860 NM_024469:Bhlhe41 − NM_024469 Bhlhe41 chr7 89111547 89137185 NM_007562:Bnc1 − NM_007562 Bnc1 chr7 133021932 133225925 NM_001101488:Gsg11 − NM_001101488 Gsg1l chr7 26472020 26490015 NM_011577:Tgfb1 + NM_011577 Tgfb1 chr7 148106800 148114439 NM_001081389:Nlrp6 + NM_001081389 Nlrp6 chr7 150293158 150612947 NM_008434:Kcnq1 + NM_008434 Kcnq1 chr7 31827533 31836473 NM_022007:Fxyd7 − NM_022007 Fxyd7 chr7 31836696 31840675 NM_052992:Fxyd1 − NM_052992 Fxyd1 chr7 31836696 31840675 NM_019503:Fxyd1 − NM_019503 Fxyd1 chr7 31836696 31839872 NM_194321:Fxyd1 − NM_194321 Fxyd1 chr7 31836696 31839872 NM_052991:Fxyd1 − NM_052991 Fxyd1 chr7 53651866 53694074 NM_001112739:Kcnc1 + NM_001112739 Kcnc1 chr7 53651837 53688723 NM_008421:Kcnc1 + NM_008421 Kcnc1 chr7 56886868 56892205 NM_001005232:Dbx1 − NM_001005232 Dbx1 chr7 57167069 57214863 NM_148931:Slc6a5 + NM_148931 Slc6a5 chr7 57165668 57214863 NM_001146013:Slc6a5 + NM_001146013 Slc6a5 chr7 105987354 106003257 NM_009519:Wnt11 + NM_009519 Wnt11 chr7 107154913 107183236 NM_133709:Chrdl2 + NM_133709 Chrdl2 chr7 138079716 138129172 NM_019564:Htra1 + NM_019564 Htra1 chr7 138686476 138688445 NM_008257:Hmx3 + NM_008257 Hmx3 chr7 138697575 138700096 NM_145998:Hmx2 + NM_145998 Hmx2 chr7 139787921 139791320 NM_009123:Nkx1-2 − NM_009123 Nkx1-2 chr7 147232055 147234987 NM_010836:Msx3 − NM_010836 Msx3 chr7 149836672 149843386 NM_001122737:Igf2 − NM_001122737 Igf2 chr7 149836672 149846940 NM_001122736:Igf2 − NM_001122736 Igf2 chr7 149836672 149844709 NM_010514:Igf2 − NM_010514 Igf2 chr7 149845597 149856261 NR_002855:Igf2as + NR_002855 Igf2as chr7 152024516 152029253 NM_008007:Fgf3 + NM_008007 Fgf3 chr8 15892544 17535385 NM_053171:Csmd1 − NM_053171 Csmd1 chr8 87231497 87298268 NM_001081981:Nfix − NM_001081981 Nfix chr8 87231497 87324239 NM_010906:Nfix − NM_010906 Nfix chr8 87231497 87324239 NM_001081982:Nfix − NM_001081982 Nfix chr8 124254462 124314721 NM_020605:Jph3 + NM_020605 Jph3 chr8 11453976 11478499 NM_011227:Rab20 − NM_011227 Rab20 chr8 12385770 12436732 NR_027975:Gm5607 + NR_027975 Gm5607 chr8 47377401 47380025 NM_173789:Helt − NM_173789 Helt chr8 72404264 72411291 NM_026818:Cilp2 − NM_026818 Cilp2 chr8 73017054 73027980 NM_018827:Crlf1 + NM_018827 Crlf1 chr8 74213150 74214476 NM_013564:Insl3 + NM_013564 Insl3 chr8 80956907 80960551 NM_138944:Pou4f2 − NM_138944 Pou4f2 chr8 86535413 86535532 NR_035431:Mir1199 − NR_035431 Mir1199 chr8 87470889 87480502 NM_144929:Rtbdn + NM_144929 Rtbdn chr8 107793773 107799745 NM_011939:Hsf4 + NM_011939 Hsf4 chr8 123651584 123654544 NM_008024:Foxl1 + NM_008024 Foxl1 chr8 123640070 123642794 NM_013519:Foxc2 + NM_013519 Foxc2 chr8 123608373 123610779 NM_010426:Foxf1a + NM_010426 Foxf1a chr8 125641273 125659085 NM_170684:Cpne7 + NM_170684 Cpne7 chr8 127316918 127358604 NM_198632:Trim67 + NM_198632 Trim67 chr9 20970157 21017692 NM_183408:Pde4a + NM_183408 Pde4a chr9 31653628 31720870 NM_013800:Barx2 − NM_013800 Barx2 chr9 32229792 32348953 NM_008026:Fli1 − NM_008026 Fli1 chr9 37223629 37240760 NM_001164767:Robo3 − NM_001164767 Robo3 chr9 49148766 49215319 NM_010077:Drd2 + NM_010077 Drd2 chr9 74709727 74737454 NM_008262:Onecut1 + NM_008262 Onecut1 chr9 79446797 79566485 NM_007730:Col12a1 − NM_007730 Col12a1 chr9 89804612 89921817 NM_011245:Rasgrf1 + NM_011245 Rasgrf1 chr9 101824457 102257023 NM_173447:Ephb1 − NM_173447 Ephb1 chr9 101824457 102257023 NM_001168296:Ephb1 − NM_001168296 Ephb1 chr9 111214242 111298279 NM_001164659:Trank1 + NM_001164659 Trank1 chr9 119392528 119488134 NM_021544:Scn5a − NM_021544 Scn5a chr9 121486960 121550684 NM_026915:Lyzl4 − NM_026915 Lyzl4 chr9 30750147 30770443 NM_013906:Adamts8 + NM_013906 Adamts8 chr9 40682209 40686055 NM_178245:Bsx + NM_178245 Bsx chr9 58044103 58049522 NM_001161537:Islr2 − NM_001161537 Islr2 chr9 58044103 58049606 NM_001161540:Islr2 − NM_001161540 Islr2 chr9 58044103 58050092 NM_001161536:Islr2 − NM_001161536 Islr2 chr9 58044103 58050092 NM_177193:Islr2 − NM_177193 Islr2 chr9 58044103 58050341 NM_001161538:Islr2 − NM_001161538 Islr2 chr9 58050703 58056615 NR_033522:1600029O15Rik + NR_033522 1600029O15Rik chr9 58044103 58052126 NM_001161541:Islr2 − NM_001161541 Islr2 chr9 58044103 58050151 NM_001161539:Islr2 − NM_001161539 Islr2 chr9 58044103 58049522 NM_001161535:Islr2 − NM_001161535 Islr2 chr9 87597634 87626095 NM_023814:Tbx18 − NM_023814 Tbx18 chr9 89804612 89810685 NM_001039655:Rasgrf1 + NM_001039655 Rasgrf1 chr9 95460235 95462540 NM_198414:Paqr9 + NM_198414 Paqr9 chr9 99774524 99776589 NM_011440:Sox14 − NM_011440 Sox14 chr9 118387306 118395250 NM_001164789:Eomes + NM_001164789 Eomes chr9 118387306 118395250 NM_010136:Eomes + NM_010136 Eomes chr9 121551833 121582072 NM_011703:Vipr1 + NM_011703 Vipr1 chr10 29172912 29255673 NM_028351:Rspo3 − NM_028351 Rspo3 chr10 61301245 61441856 NM_007731:Col13a1 − NM_007731 Col13a1 chr10 79819203 79828234 NM_183152:Plk5 + NM_183152 Plk5 chr10 126609481 126617701 NM_177615:Slc26a10 − NM_177615 Slc26a10 chr10 19076344 19078410 NM_053008:Olig3 + NM_053008 Olig3 chr10 19567722 19571265 NM_029529:Slc35d3 − NM_029529 Slc35d3 chr10 22537078 22539934 NM_011545:Tcf21 − NM_011545 Tcf21 chr10 42281776 42303394 NM_152229:Nr2e1 − NM_152229 Nr2e1 chr10 61595837 61597511 NM_009719:Neurog3 + NM_009719 Neurog3 chr10 67000616 67004936 NM_010118:Egr2 + NM_010118 Egr2 chr10 79803460 79811191 NM_001113548:Adamtsl5 − NM_001113548 Adamtsl5 chr10 79805483 79811157 NM_025629:Adamtsl5 − NM_025629 Adamtsl5 chr10 79957650 79980005 NM_139226:Onecut3 + NM_139226 Onecut3 chr10 86953785 86956405 NM_008553:Ascl1 − NM_008553 Ascl1 chr10 126760782 126766999 NM_146011:Arhgap9 + NM_146011 Arhgap9 chr10 126962528 126971615 NM_183297:Nxph4 − NM_183297 Nxph4 chr11 23978055 24073558 NM_016707:Bcl11a + NM_016707 Bcl11a chr11 23980694 24073558 NM_001159290:Bcl11a + NM_001159290 Bcl11a chr11 23978055 24073558 NM_001159289:Bcl11a + NM_001159289 Bcl11a chr11 85710266 85729599 NM_172798:Tbx4 + NM_172798 Tbx4 chr11 85703564 85729599 NM_011536:Tbx4 + NM_011536 Tbx4 chr11 103635488 103679335 NM_009521:Wnt3 + NM_009521 Wnt3 chr11 107596093 107655778 NM_019431:Cacng4 − NM_019431 Cacng4 chr11 33100751 33103588 NM_019916:Tlx3 − NM_019916 Tlx3 chr11 57642214 57645649 NM_008213:Hand1 − NM_008213 Hand1 chr11 59061543 59104253 NM_009522:Wnt3a − NM_009522 Wnt3a chr11 69617096 69619126 NM_001033433:Tmem102 − NM_001033433 Tmem102 chr11 71861029 71949391 NM_001081641:Pitpnm3 − NM_001081641 Pitpnm3 chr11 71861029 71949391 NM_001024927:Pitpnm3 − NM_001024927 Pitpnm3 chr11 75582591 75609559 NM_007873:Doc2b − NM_007873 Doc2b chr11 76812098 76845845 NM_010484:Slc6a4 + NM_010484 Slc6a4 chr11 85646116 85655450 NM_009324:Tbx2 + NM_009324 Tbx2 chr11 94981430 94986605 NM_010055:Dlx3 + NM_010055 Dlx3 chr11 95001760 95007115 NM_007867:Dlx4 − NM_007867 Dlx4 chr11 95371159 95375879 NM_130858:Nxph3 − NM_130858 Nxph3 chr11 95724872 95776185 NM_008081:B4galnt2 − NM_008081 B4galnt2 chr11 96055674 96057913 NM_008267:Hoxb13 + NM_008267 Hoxb13 chr11 96160484 96162883 NM_008269:Hoxb6 + NM_008269 Hoxb6 chr11 96132643 96137907 NM_008270:Hoxb9 + NM_008270 Hoxb9 chr11 96126477 96126579 NR_029721:Mir196a-1 + NR_029721 Mir196a-1 chr11 96147959 96151477 NM_010460:Hoxb7 + NM_010460 Hoxb7 chr11 96143218 96146639 NM_010461:Hoxb8 + NM_010461 Hoxb8 chr11 98186730 98190959 NM_010895:Neurod2 − NM_010895 Neurod2 chr11 100939724 100941819 NM_010475:Hsd17b1 + NM_010475 Hsd17b1 chr11 101823771 101828329 NM_024449:Sost − NM_024449 Sost chr11 103588676 103611135 NM_011719:Wnt9b − NM_011719 Wnt9b chr11 103994195 104036832 NM_007762:Crhr1 + NM_007762 Crhr1 chr11 115176505 115183232 NM_176847:Ush1g − NM_176847 Ush1g chr11 116142252 116145252 NM_010254:Galr2 + NM_010254 Galr2 chr11 116396053 116397989 NM_011451:Sphk1 + NM_011451 Sphk1 chr11 116393757 116397989 NM_001172472:Sphk1 + NM_001172472 Sphk1 chr11 116393757 116397989 NM_001172473:Sphk1 + NM_001172473 Sphk1 chr11 116393224 116397989 NM_001172475:Sphk1 + NM_001172475 Sphk1 chr11 116394551 116397989 NM_025367:Sphk1 + NM_025367 Sphk1 chr11 118938884 118947551 NM_007625:Cbx4 − NM_007625 Cbx4 chr11 120392040 120400298 NM_008101:Gcgr + NM_008101 Gcgr chr11 120515102 120522151 NM_175263:Notum − NM_175263 Notum chr12 11097007 11157648 NM_001168564:Kcns3 − NM_001168564 Kcns3 chr12 11097007 11157179 NM_173417:Kcns3 − NM_173417 Kcns3 chr12 57796625 57812217 NM_011041:Pax9 + NM_011041 Pax9 chr12 87762593 87862578 NM_011934:Esrrb + NM_011934 Esrrb chr12 103367628 103504959 NM_172152:Slc24a4 + NM_172152 Slc24a4 chr12 8304723 8308760 NM_013527:Gdf7 − NM_013527 Gdf7 chr12 9581247 9588306 NM_011859:Osr1 + NM_011859 Osr1 chr12 56699903 56703004 NM_020287:Insm2 + NM_020287 Insm2 chr12 57632923 57636093 NM_001146198:Nkx2-1 − NM_001146198 Nkx2-1 chr12 57632923 57637895 NM_009385:Nkx2-1 − NM_009385 Nkx2-1 chr12 59312790 59317023 NM_009216:Sstr1 + NM_009216 Sstr1 chr12 74040931 74045886 NM_011384:Six6 + NM_011384 Six6 chr12 85910801 85936407 NM_007701:Vsx2 + NM_007701 Vsx2 chr12 105709418 105711446 NM_010351:Gsc − NM_010351 Gsc chr12 112680871 112693229 NM_009396:Tnfaip2 + NM_009396 Tnfaip2 chr13 73397944 73407068 NM_018885:Irx4 + NM_018885 Irx4 chr13 13876805 13920162 NM_010317:Gng4 + NM_010317 Gng4 chr13 48758404 48761876 NM_007526:Barx1 + NM_007526 Barx1 chr13 51526410 51662453 NM_009167:Shc3 − NM_009167 Shc3 chr13 22094044 22101610 NM_019429:Prss16 − NM_019429 Prss16 chr13 31650038 31652843 NM_008239:Foxq1 + NM_008239 Foxq1 chr13 31898514 31902504 NM_008592:Foxc1 + NM_008592 Foxc1 chr13 40811043 40825812 NM_001122948:Tcfap2a − NM_001122948 Tcfap2a chr13 40811043 40829192 NM_011547:Tcfap2a − NM_011547 Tcfap2a chr13 56351859 56353524 NM_010896:Neurog1 − NM_010896 Neurog1 chr13 95645581 95653636 NM_011021:Otp + NM_011021 Otp chr13 99124199 99126660 NM_008242:Foxd1 + NM_008242 Foxd1 chr13 113827741 113827832 NR_029961:Mir449a + NR_029961 Mir449a chr13 113784075 113790602 NM_001037914:Gm6320 + NM_001037914 Gm6320 chr13 113826190 113826299 NR_030452:Mir449c + NR_030452 Mir449c chr13 113827626 113827706 NR_030602:Mir449b + NR_030602 Mir449b chr13 117088477 117099896 NM_021459:Isl1 − NM_021459 Isl1 chr14 58691522 58731557 NM_013518:Fgf9 + NM_013518 Fgf9 chr14 30853124 31166672 NM_001083616:Cacna1d − NM_001083616 Cacna1d chr14 63817751 63864097 NM_008092:Gata4 − NM_008092 Gata4 chr14 67852128 68048604 NM_010095:Ebf2 + NM_010095 Ebf2 chr14 13174405 13178379 NM_080433:Fezf2 − NM_080433 Fezf2 chr14 33221388 33279095 NM_009891:Chat − NM_009891 Chat chr14 33275622 33278036 NM_021712:Slc18a3 − NM_021712 Slc18a3 chr14 57717438 57723539 NM_008125:Gjb2 − NM_008125 Gjb2 chr14 65209493 65209578 NR_029813:Mir124a-1 + NR_029813 Mir124a-1 chr14 67254094 67352166 NM_013461:Adra1a + NM_013461 Adra1a chr14 69790075 69793597 NM_010920:Nkx2-6 + NM_010920 Nkx2-6 chr14 70477251 70479964 NM_018781:Egr3 + NM_018781 Egr3 chr14 70953862 70973349 NM_021877:Hr + NM_021877 Hr chr15 72342548 72376709 NM_001033876:Kcnk9 − NM_001033876 Kcnk9 chr15 11769651 11835429 NM_008728:Npr3 − NM_008728 Npr3 chr15 11769651 11835429 NM_001039181:Npr3 − NM_001039181 Npr3 chr15 64530596 64753858 NM_009623:Adcy8 − NM_009623 Adcy8 chr15 73617365 73670101 NM_001033365:Gm628 − NM_001033365 Gm628 chr15 78500436 78548543 NM_183141:Elfn2 − NM_183141 Elfn2 chr15 10963471 10967723 NM_178717:Rxfp3 − NM_178717 Rxfp3 chr15 31221234 31297514 NM_027496:Ankrd33b − NM_027496 Ankrd33b chr15 31253709 31297514 NM_026153:Ankrd33b − NM_026153 Ankrd33b chr15 31221234 31297514 NM_001164441:Ankrd33b − NM_001164441 Ankrd33b chr15 74346625 74419894 NM_174991:Bai1 + NM_174991 Bai1 chr15 75395174 75397612 NM_011837:Ly6h − NM_011837 Ly6h chr15 75395174 75397078 NM_001135689:Ly6h − NM_001135689 Ly6h chr15 75395174 75397286 NM_001135688:Ly6h − NM_001135688 Ly6h chr15 75577272 75578352 NM_194350:Mafa − NM_194350 Mafa chr15 85365866 85411159 NM_001163633:Wnt7b − NM_001163633 Wnt7b chr15 85365866 85412251 NM_009528:Wnt7b − NM_009528 Wnt7b chr15 85365866 85408500 NM_001163634:Wnt7b − NM_001163634 Wnt7b chr15 98465194 98474961 NM_007581:Cacnb3 + NM_007581 Cacnb3 chr15 98462650 98474961 NM_001044741:Cacnb3 + NM_001044741 Cacnb3 chr15 98620287 98624261 NM_021279:Wnt1 + NM_021279 Wnt1 chr15 98602182 98608581 NM_011718:Wnt10b − NM_011718 Wnt10b chr15 98723457 98728971 NM_007857:Dhh − NM_007857 Dhh chr15 99055406 99073248 NM_010601:Kcnh3 + NM_010601 Kcnh3 chr15 99421458 99425260 NM_009701:Aqp5 + NM_009701 Aqp5 chr15 99501148 99531559 NM_009597:Accn2 + NM_009597 Accn2 chr15 100451770 100467286 NM_174992:Smagp − NM_174992 Smagp chr15 100451770 100467296 NM_001033872:Smagp − NM_001033872 Smagp chr16 35541447 35664344 NM_013661:Sema5b + NM_013661 Sema5b chr16 11984205 12270997 NM_001174086:Shisa9 + NM_001174086 Shisa9 chr16 11984205 12270997 NM_028277:Shisa9 + NM_028277 Shisa9 chr16 35155721 35304635 NM_001012765:Adcy5 + NM_001012765 Adcy5 chr16 44240292 44332951 NM_001159419:Sidt1 − NM_001159419 Sidt1 chr16 44240292 44332951 NM_198034:Sidt1 − NM_198034 Sidt1 chr16 94085504 94348638 NM_011377:Sim2 + NM_011377 Sim2 chr16 17797374 17808380 NM_153790:Scarf2 + NM_153790 Scarf2 chr16 17913646 17915152 NM_029469:Gsc2 − NM_029469 Gsc2 chr16 18581805 18587062 NM_011532:Tbx1 − NM_011532 Tbx1 chr16 20589654 20598540 NM_182636:Vwa5b2 + NM_182636 Vwa5b2 chr16 20589654 20605450 NM_001144953:Vwa5b2 + NM_001144953 Vwa5b2 chr17 8994609 9179513 NM_011866:Pde10a + NM_011866 Pde10a chr17 14416512 14541797 NM_022315:Smoc2 + NM_022315 Smoc2 chr17 8627287 8635361 NM_009309:T + NM_009309 T chr17 23878165 23882796 NM_028416:Kremen2 − NM_028416 Kremen2 chr17 26975609 26978510 NM_008700:Nkx2-5 − NM_008700 Nkx2-5 chr17 46434369 46440220 NM_207666:Dlk2 + NM_207666 Dlk2 chr17 46579396 46624624 NM_001162864:Ttbk1 − NM_001162864 Ttbk1 chr17 56650670 56651906 NM_011483:Znrf4 − NM_011483 Znrf4 chr17 57418522 57468659 NM_001163816:Vav1 + NM_001163816 Vav1 chr17 57418522 57468659 NM_011691:Vav1 + NM_011691 Vav1 chr17 57418522 57468659 NM_001163815:Vav1 + NM_001163815 Vav1 chr17 80106292 80114381 NM_009994:Cyp1b1 − NM_009994 Cyp1b1 chr17 86083607 86087594 NM_011380:Six2 − NM_011380 Six2 chr17 86006697 86017705 NR_015387:Six3os1 − NR_015387 Six3os1 chr17 86010602 86017615 NR_015386:Six3os1 − NR_015386 Six3os1 chr17 86014726 86018751 NR_015385:Six3os1 − NR_015385 Six3os1 chr17 86020173 86025531 NM_011381:Six3 + NM_011381 Six3 chr17 88145160 88197334 NM_199251:Kcnk12 − NM_199251 Kcnk12 chr17 93598761 93604829 NM_009625:Adcyap1 + NM_009625 Adcyap1 chr18 22851655 23197164 NM_001161483:Nol4 − NM_001161483 Nol4 chr18 66216509 66451492 NM_178793:Ccbe1 − NM_178793 Ccbe1 chr18 67293479 67386445 NM_010307:Gnal + NM_010307 Gnal chr18 74602272 74931131 NM_201600:Myo5b + NM_201600 Myo5b chr18 80802943 80904912 NM_001164111:Nfatc1 − NM_001164111 Nfatc1 chr18 80802943 80904912 NM_001164112:Nfatc1 − NM_001164112 Nfatc1 chr18 80802943 80909810 NM_198429:Nfatc1 − NM_198429 Nfatc1 chr18 80802943 80909810 NM_001164110:Nfatc1 − NM_001164110 Nfatc1 chr18 80844173 80904912 NM_016791:Nfatc1 − NM_016791 Nfatc1 chr18 80844173 80909810 NM_001164109:Nfatc1 − NM_001164109 Nfatc1 chr18 82561887 82576169 NM_008082:Galr1 − NM_008082 Galr1 chr18 37303622 37347311 NM_001003672:Pcdhac2 + NM_001003672 Pcdhac2 chr18 42554250 42555747 NM_138945:Pou4f3 + NM_138945 Pou4f3 chr18 53624199 53735511 NM_001033281:Prdm6 + NM_001033281 Prdm6 chr18 66094292 66098743 NM_013833:Rax − NM_013833 Rax chr18 77095143 77139081 NM_001109743:Skor2 + NM_001109743 Skor2 chr18 81163112 81183317 NM_178280:Sall3 − NM_178280 Sall3 chr19 42863084 43462801 NM_001081257:Hpse2 − NM_001081257 Hpse2 chr19 25685026 25698411 NM_177360:Dmrt3 + NM_177360 Dmrt3 chr19 5549136 5560575 NM_019935:Ovol1 − NM_019935 Ovol1 chr19 16946805 16948320 NM_008023:Foxb2 − NM_008023 Foxb2 chr19 43686814 43690382 NM_008699:Nkx2-3 + NM_008699 Nkx2-3 chr19 44831883 44910517 NM_011037:Pax2 + NM_011037 Pax2 chr19 45225204 45231433 NM_021901:Tlx1 + NM_021901 Tlx1 chr19 45308217 45309726 NM_010691:Lbx1 − NM_010691 Lbx1 chr19 45811287 45817374 NM_001166363:Fgf8 − NM_001166363 Fgf8 chr19 45811287 45817374 NM_001166361:Fgf8 − NM_001166361 Fgf8 chr19 45811287 45817374 NM_010205:Fgf8 − NM_010205 Fgf8 chr19 45811287 45817374 NM_001166362:Fgf8 − NM_001166362 Fgf8 chr19 46210175 46222815 NM_008852:Pitx3 − NM_008852 Pitx3 chr19 54119671 54123472 NM_007417:Adra2a + NM_007417 Adra2a chr19 59240676 59244519 NM_009501:Vax1 − NM_009501 Vax1

TABLE S6 Accession numbers of all datasets used in this study Factor Background Data Accession Accession Type Factor Cell Type Number Number ChIP-seq SMC1 ESC GSM560341, GSM1082343 GSM560342 ChIP-seq CTCF ESC GSM747534, GSM747545, GSM747535, GSM747546 GSM747536 ChIP-seq Pol2 ESC GSM515670, GSM1082343 GSM515672 ChIP-seq OCT4 ESC GSM1082340 GSM1082343 ChIP-seq SOX2 ESC GSM1082341 GSM1082343 ChIP-seq NANOG ESC GSM1082342 GSM1082343 ChIP-seq KLF4 ESC GSM288354 GSM1082343 ChIP-seq ESRRB ESC GSM288355 GSM1082343 ChIP-seq MED1 ESC GSM560348 GSM1082343 ChIP-seq MED12 ESC GSM560345, GSM1082343 GSM560346 ChIP-seq H3K27ac ESC GSM594579 GSM1082343 ChIP-seq H3K4me3 ESC GSM1082344, GSM1082344 GSM307149 ChIP-seq H3K36me3 ESC GSM307153 GSM1082345 ChIP-seq H3K27me3 ESC GSM1397343 GSM1082343 ChIP-seq SUZ12 ESC GSM480162 GSM480164 ChIP-seq EZH2 ESC GSM480161 GSM480164 ChIP-seq SOX2 NPC GSM1050288, GSM1050290 GSM1050289 ChIP-seq BRN2 NPC GSM1050286, GSM1050290 GSM1050287 ChIP-seq SMC1 NPC GSM883646 GSM883648 ChIP-seq CTCF NPC GSM883647 GSM883648 RNA-seq none ProB SRR499680 none RNA-seq none Th1 SRR557795 none RNA-seq none C2C12 SRR496442 none RNA-seq none macrophage SRR836120 none ChIA-PET SMC1 ESC GSM1397342 none ChIA-PET SMC1 ESC GSM1480237 none

LENGTHY TABLES

The patent application contains a lengthy table section. A copy of the tables are available in electronic form from the USPTO web site. An electronic copy of the tables will also be available from the USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

The Tables referenced herein were previously submitted in U.S. Provisional Application No. 62/234,770, and are hereby incorporated by reference in their entirety. 

We claim:
 1. A method of altering the expression of a gene in an insulated neighborhood (IN) of the genome of a cell comprising contacting an organism comprising said cell with a gene modulatory molecule.
 2. The method of claim 1, wherein the gene modulatory molecules is selected from the group consisting of a small molecule, lipid, protein, peptide, nucleic acid and combinations thereof.
 3. The method of claim 2, wherein the expression of the gene is increased.
 4. The method of claim 3, wherein the cell is selected from the group consisting of stem cells, bone marrow cells, testis cells, olfactory cells, lung cells, thymus cells, cells of the central nervous system, cells of the brain, spleen cells, MEF cells, MEL cells, heart cells, somatic cells of the limbs, liver cells, and kidney cells.
 5. The method of claim 4, wherein the cells are stem cells and said stem cells are embryonic stem cells.
 6. The method of claim 1, wherein the insulated neighborhood comprises a topologically active domain (TAD).
 7. The method of claim 6, herein the topologically active domain is a super-enhancer domain (SD).
 8. The method of claim 7, wherein the SD is selected from the group consisting of those of Table S4A and S4B.
 9. The method of claim 1, wherein the gene is selected from the group consisting of those in Table S4C.
 10. A method of altering the expression of a gene located in an insulated neighborhood (IN) of the genome of a cell comprising altering the sequence of one or more of the CTCF boundaries of said insulated neighborhood.
 11. The method of claim 10, wherein the insulated neighborhood (IN) is a topologically active domain (TAD).
 12. The method of claim 11, wherein the topologically active domain is a super-enhancer domain (SD).
 13. The method of claim 12, wherein the SD is selected from the group consisting of those of Table 54A and S4B.
 14. The method of claim 10, wherein the CTCF boundary is altered via CRISPR technology.
 15. The method of claim 14, wherein only the sequence of the 5′ CTCF boundary of said insulated neighborhood is altered.
 16. The method of claim 14, wherein alteration comprises deletion of said one or more CTCF boundary.
 17. The method of claim 10, wherein the cell is selected from the group consisting of stem cells, bone marrow cells, testis cells, olfactory cells, lung cells, thymus cells, cells of the central nervous system, cells of the brain, spleen cells, MEF cells, MEL cells, heart cells, somatic cells of the limbs, liver cells, and kidney cells.
 18. The method of claim 17, wherein the cells are stem cells and said stem cells are embryonic stem cells. 